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Nanopore sequencing .

This document discusses nanopore sequencing technology. It provides an overview of nanopore sequencing, including what nanopore sequencing is, the types of nanopores used (biological and solid state), advantages such as not requiring amplification or labeling, and challenges with processing large amounts of raw data. The document then examines raw nanopore data and the initial steps needed to process the data, including creating a training data set to predict genomic bases and releasing analysis packages to the community.

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S ADAM University of Kyrgyz Republic. Faculty of medicine Nanopore Sequencing Student: Tashfeen Ahmad Group:GM_4 Teacher: Prof. Domashov Iliya
Nanopore Sequencing Outline • Nanopore Sequencing Technology • Raw Data • Transformations and Raw Data Processing • Toward Producing a Basecaller • Future Directions
What is Nanopore Sequencing? Determine the sequence of DNA fragments by passing DNA through a protein (or other) pore in a membrane Nanopore sequencing is a third generation[1] approach used in the sequencing of biopolymers - specifically, polynucleotides in the form of DNA or RNA.
What is Nanopore Sequencing? Oxford Nanopore became the first company to provide a commercially available nanopore sequencer in 2015 (available to community in 2012)
What is Nanopore Sequencing? Nanopore is a disruptive technology: • Sequencer Size • Read Length • Potential direct RNA sequencing • Biology Problem with Data Velocity Issues • Currently ~400GB/24 hours needs to be processed
Adventages S Using nanopore sequencing, a single molecule of DNA or RNA can be sequenced without the need for PCR amplification or chemical labeling of the sample. S At least one of these aforementioned steps is necessary in the procedure of any previously developed sequencing approach. S Nanopore sequencing has the potential to offer relatively low- cost genotyping, high mobility for testing, and rapid processing of samples with the ability to display results in real-time.
Adventages S Publications on the method outline its use in rapid identification of viral pathogens,monitoring ebola, environmental monitoring, food safety monitoring, human genome sequencing, plant genome sequencing,monitoring of antibiotic resistance, haplotyping and other applications.
Types S Biological nanopore S Solid state nanopore
Biological Nanopore S Also called Transmembrane protein channels S Usually inserted into a subtrate such as planner lipid bilayer liposomes or other polymer films S E.g alpha hemolysin , MspA ,
Solid State Nanopore S Made in Silicon Compond membrane (silicon Nitride)
Raw Nanopore Data
Processing Raw Data • First step is to create a training data set • Starting from provided raw data followed by processing to produce useful data set for training to predict genomic bases • Goal is to release this package to the community for greater access to create training data sets for this data
Poorly Documented Metadata
Raw Nanopore Data G G G G GGG GG G GG G G GGGGG G G GG GG G G G G GG T T T T T T T T T T TTT TT TT T T T T T T TTT T T T T T TTT T T TT T T T TT T TT T TT T T TT TT T T TTT T T T T T T TTTTTTTTT T T T T T T T TT T TT T TTT T T T T TT T T TT T T T C C CCCCCC C C CCC CCCCCC CCCCCCCCC C CCCCC CCC C CC CCCCCCCCCC CCC C C C C CCCCCCCCCCCCCCCCC C CCCCC CCCCCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA A AAA GGGGGG G GGG GGGG GG G GG G AAAAA A AA AA A AAAA AAA A A A A AA A A AAA A AA A AA A A A A AA A AA A A AA A A A A A A A A AA AA A A A A AA A AA A AAAA A A AA A AA A A AAA A A AA A A A AA AA AA A A A A AA A A AAAA A AA AA AA AA A A AA A AAAAA A A AA AAAAAA AA A A AAAAA AAA AAAAAAAAAAAAAAA A A A A A T TTT TTTTTTTTTTTTT TTTTTTT T TTTTTT TTTT TTTTTTTTTTTT TTTTTTTTTTT T TTTTTTT T TTTTTTTTTT TTT TT TTTTTTTTTTTTTTTTTTTTT TTTT TTTTTTTT TTTTTTTTTTTTT TTTTTT TT T T TTT T T TTTTTTTTTTTTTTTTT CCCCCCC CCCCC C C CCCCCC C CCCCCCCCCCCCCCCCCC AA A A A AAAAAAAA AAA A A G G GGGGGG GGGG G TT T T T T T T TT T T GGGGGG G GGGGGGGG G GGGG G GG G GGGGG GG G G G GG GGGGGGG GGGGG G GG G G G GG G G GG G G G GG G GGGGG G G G GGG G G G GG TTT T T TTT T T T T TTT TT T T T T T T T TTTT T T T T T T T T TT T TTTT T GG G G G G GGGGGG G GGG GGGG G GGG G GGG G C C CC C CC CC C CC CC CCCCC C CCC AAA A A A AAAA AAAA A AAA AA A AA A AA AA AA T TTTTTTTTTTTTTTTTT TTTTTTTTTT T T TTTT TTT T T T C C CC CC C C C C CCC CCCCCCCC C C CCCC C CCCC C CC CCCC C CCCCCC C CCC CCCCCC CCCC CC C CC CCCCCC CCC C C CC CCCC C C C C CC CCCCCCCCCCCC CCC CCCCC CCCCCCCC CC CCCCC CCCCCCCCCCCCCCC CCCCCCC CCCC CCCCC C CCCCCCCC CCC C CC C CCCC GGGGGGGGGG GGGG GG GGGGG G G G GGGGGGG GGGGGGGG GGGGGGG GGGGGGGGG GGGGGG GG G GGG T T TTT T T G G GGG G G G GG GG G G GG GG GGG G G AAAA AA AAAAAA A AAAAA AAAAA C CCCCCCCC CCC GGGGG GGGG GGGG G GGGGG GG G GG GGG GGGGGGGGGGG G GGG G GGGGGGGGGGG GGG G A AA AAAAAAAAAAAAA AA AAA A A T T TT T TTTTTTTTTTT T CC C CCCC CCCCCC CC CCCCCC CCCCCCGGGGG G G GGG GGGGGGGG GGGGG G GGGG G GGG G GGGGGGGG GG G GGGGG G G G GGGG G G GGG G GGGGGGGGGGGG G GGGGG G GGGGGGGGG G G GGGG G GGGG GGGGGGG G G G GGG G G GG GG GGG G GG GGG GG GGGGGGGG GGGG G GGG GGGGGGG GGGG GGGG G GGGGGG G G G GGGGGGGG G G G GG G G GGGGGG GGGGGGG G G G G G GGGG GG G GG GGGGGG G GGGGGGG G GGG G GAA AAAAAA AAAAAA A A AAA AA AAAAAA G G G G GG G G GGG G GG G GG G G G G G G G GGG G GGGG G GGG GG GG G CC C CC C C C C C CC C C G G G G G G GG GGG G G G G G G G G G G G G G G G G GGGG G T T TT TT T T T T TT T T TTT TT T T T T TTTTTT TTT T T TT T T TTT T T T T T T T T T T TT TTT T TT T TT T T T T T TT T T C C C CCC C CC C C C C C C C C C C CC C CC CCCC C C C CC C GG G GG GG G G G GGGG GGG G G GG GGGG G G GG G G G GG G T T T T T T T T T T T T T TT T T T T TT T T TT TT T T T T T TT TT T T T T TT T T TT T T T T TTT T TTT TTT TT TTT T T T AA A A AAAAA AAAAAA A AAA A AAAAAA A AAAA A AAAAAAAAAAAAA AAAA AAAA A AAA AAAAAAA AAA AAAAA AA AAAAAAA A AAA A AAA A AAAAAAAAAAA AA AAAAA AAAAAAAAAAAAAAAA A A AAAAA AAA A A A A AAAA AAAAAAAA AAAAAA A T TT T T TTTTT T TTTT T T T TTT T TTTT T T TTTT T TTT TTTTTTT TT T TT TT TTTT T TT T T TTTTT TTTTTT A A AAAAAAAAAAAAA AAAAAAAAAAA AAAAA AA AAAAAAA AAAAAA AAAA A A AAAA AAA AAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA A AAGG GGGGGGGGGGGGG GGGGGGGGG GGG TTTTTTTTTTTT TTTT TTTT T TTT TTT T TTTTTT T TTTTTTTT T TT T TTTTTTTTTTT TTTT TTTT T T TTT T TTTT T TTTTTTTT TT TTT TT T TTTTTT T T T TTTT TTTTTT T T T TTT AAA AAAAAA AA AAAAAAAAAAAA AAAA AAAAAAAAAAAA AAAAAAAAAAAAAAA AA A AAAAAAAAAAA AAAAAAAAA AAAA AAAA A A AA A AAA AAAAAAAA AAAAAAAAAAAA AAAAAAAAAAAAAA AAAAAAAAAAAAA A AAA AAAA AA A AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA CCCCCCCCCCCCCCCCCCCCCC CC CCCCCCCC C CCCCCC CCCC CCCCCCCCCCCC CC C CC CC CCC CCC CCCCCC CCCC C C CCC C CCC C CCCCCCCC CCCC T T TT T T T TTT T TTTTT T T T T TT TTT T TT T TTT T T T TT TTT T T TT T T T T TT T T T TTTTTT T TT T T TTTT T TT T T T T TTTTT T TT T T T T T T T TTTTT TTTTTTTTT TT T T TTT T TTTT T TTTTTTT T TTT TTTTTTT T TTT TT TTTT T TT TTTTTTTTTTT T T T T TTT TT T T T TTTTTTT TT T TTTT T TTTT T TTTTT T T T C C CCCCCCCCCCCCCCC TTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTT TTTT T T G G G G GG G G G G G G G G G G G GG G G GG G GG G G G GG G GGG GGGGG G G G G G T T TT T T T T T T T TTT T T T T T T A A A AAAAAAAAAA AAAAAAAAAAAAAAAA AAAAA A AAAAA TT TTTT TT TTTTTTTTTTTTTTTTTTTTTT T TTTTTTTTTT TTTTT TTTTTTTTTT TTTTTTTTTTTT TTTTTTTTTTTT GGGGG GGGGGGGGGGGGGG GGGGGGGGG G GGGGGGG G GGGGGGGGGGGGG G G G GGGGGGGGGGGGGG G G G GG GGGGGGGGG G GGGGGG GGGGGGGGG G GGGGGGGG GGGG G C CC CC C CCC C CC CCC C C C CCCCCCCCCCCCCCC C CC C AAA AAA AA A A AAAAAAAAA AA A AAAAAAAA AAAAA A A AA A AAA AAAAAAAA AA A AAAAAA AAAAAAAAA AA AA AAA AAAA A AA AAAA A A AAA A AAAAAAAAA A AAAA A A AAA A AA A A AAAAAAAA A AAAAAAA A AAAAA A A A A AAA A AAA AAAAAAAAA AAA A AAAAA A AAAADDDD DDDDDDDDDDDDDDDD DDDDDDD DDD DDDD DD D D DDDDDDDDDDD D DDDDDDDDDDDDDD DDDDDDDD D DD DD DDDDDDD DDDD D DDD DDDDDD D DDDDDDDD DDDDDD DD DD DDDDDDDDDDDDD DD D DDD DD D DDDDDDDDDD DDDDD DDD DDDDDDDDDDDDDDDDDDDDDDDD AA AA A AAAA AAAAA AAAAAAAAAAAA AAAAAAAAA A AAAAA AAAA AAAAAAAAAAAAAAAAAAAA A A A A AAAAAA AAAAA A AAAA AA AA A A AAAA AAAAAAAAAAA AAAAAAAAAAAAAAAA A AAA A AAAAAAAAAAA AAAA A AAA AAAAAAAAAAAAAAAAAAA AAAA A A AA A AAA AAAAA AAAA A A AAAAAAAAAAA AA AAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAA AAAA A AA A T TTTTTT T TTT T TTTTT AAAAAAAAAAAAAA A A D DDDDDDDD D DDD D D DD DDDD D AA A AAAAAA A AAA GGGGG GGGGG G GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG G GAATT C G G G C T300 350 400 450 500 42771000 42772000 42773000 42774000 Time Signal G GG G GGG GGGGGG GGGGGGG G GGGGG G G GGG TTTT TTTT TTTTTTTTTTTT TTTTTTTTTTTTTTT T TTT TTTTTTTTTTTT TTTT TTTTTTTTTTTTTTTTTTTTTTTTTTT TT T TTT TTTTT TTTTT TTTT T T C C C CCCCC C C C CC CCCCCC CCCCCC CCC C CCCC C CCC C CC CCCCCCCCCC CCC C C CC CCCCCCCCCCCCCCCCC C CCCCC CCCCCCAAAAAAAAAAAAAAAAAAAAAAA A AAAAA AAAAAAAAAAAAAAA A AAA GGGGGG GGGG GGGGGGGGG G AAAAAA AA AA AAAAA AAA AA AAAA A A AAA AAAAAA A A A A AA AAAA A AA AAA A A AAA AA AAA A A A AAA AA AAAAA A A AA A AA A A AAAA AAAAAA AA AA AA A A A AAA A A AAAAAAA AAAA AAAAAAAAAAAA A A AA AAAAAAAA A A AAAAAAAA AAAAAAAAAAAAAAA A A A A A T TTT TTTTTTTTTTTTT TTTTTTT T TTTTTT TTTT TTTTTTTTTTTTTTTTTTTTTTT T TTTTTTT T TTTTTTTTTT TTT TT TTTTTGGGGGGG GGGG GGGGG GGG G G GGGG G GG G G G GGGGGGGG GG GGGGGG GG G G GGG A A A AAAAAAAAAACC CCCC AA A AAA A AAAAA A A A AAAAA A AAA AAAAAAAA AAAAA AA GG GG G GGGGGGAAAAAA A T T TTTTTT TTTT T TT TT TTTTTTTT GGGGGG G GGGGGGGG G GGGG G GG G GGGGGGG G G G GGGGGGGGGGGGGG G GGG G G GG GG GG GGG GG G GGGGG G G G GGGG G GGG TTT TT TTT TTT T TTTTTT TTTT T T TTTTT TTTT T T TTTTTTTTT GG GG G GGGGGGGGGGGGGGG G GGG G GGG G C C CC C CCCC C CC CCCCCCC C CCC AAA A A A AAAA AAAA A AAA AA A AA AAA AA AA T TTTTTTTTTTTT TTTTT TTTTTTTTTT T T TTTT TTT TT T C C CCCC C C C CCCC CCCCCCCC CC CCCC CCCCC CCC CCCCC CCCCCC C CCCCCCCCCCCCCCCCCCCCCCCC CCCC CCCCCCC C C C C CC CCCCCCCCCCCC CCC C C CCC CCCCCCCC C C CCCCC CCCC CCCC CCCCCCC C CCCCCC CCCC CCCCC C CC CCCCC C CCC C C C C CCCC G GG GGGGGGG GGG G GG G GGGG G G G GGGGGGG G GG GGGGG GGGGGGG GGGGGGGGG GGGGGG GG G GGG T T TTT T T GGGGGG G GGG GG G G GGGGGGGGG A AAA AA A AAAAA A A AAAA AAAAA C CCCCCCC C CCC GGGGG GGGG GGGG G GGGGG GGGGG GGG GGGGGGGGGGG G GGG G GGGGGGGGGGGGGG G A AA AAAAAAAAA AAAA AA AAA A A T T TT T TTTT TTTTTTT T CC C CCCC CCCCCC CC CCCCC C CCCCCCGGGGG GG GGG GGGGGGGG GGGGG G GGGG G GGG G GGGGGGGG GG G GGGGG G G G GGGG G G GGGG GGGGGGGGGGGG G GGGGG GGGGGGGGGG G GGGGG G GGGG GGGGGGGG G G GGG G G GGGG GGG G GG GGG GG GGGGGGGGGGGG GGGGGGGGGGG GGGG GGGG G GGGGGG GG G GGGGGGGG G G G GG G G GGGGGG GGGGGGG G G G G G GGGG GG G GG GGGGGG G GGGGGGG G GGG G GAAAAAAAAAAAAAA A A CCC CC CCCCCC G G G GGG G G GGG G GG G GG GGGG GG G GGG G GGGGG GGG GGGG G CC CCC C C CCC CC C C G G G GGG GGGGGG G G G G GG G GG GGG G G GGGGGG TTTTTT TTT TTT T TTTTTTTTTT TTTTTTTTTT T TT TTTTTT TTTT T TTTTTTTTTTTTTTT TT TTT TT T T C CC CCCC CCCC CCCC CC CCCCCCCCCCCC CCCC C GG G GGGG G G GGGGGGGGG G GGGGGG G GGG GGG GG G TTTTTTTT T TT T TTTTT TTTTTTTTTTTTTT TTTTTTTTTTTT TTTT T TTTTTTTTTTTT TT TTTTT T GG G G GGGGG G GGGGG G GGG G GGGGGG G G GG G G GGGGGGGGGGGGG GGGG GGGG G AAA AAAAAA A AAA A AAAA AA AAAAAAA A AAA A AAA A A AAAAAAAAAA AA A AAAA AAAAAAAAAAAAAAAA A A AAAAA AAA A A A A AAAA AAAAAAA A AAAAAA A TTT T TTTTTT TTTTTT TTTTTTTTTTT TTTTT TTTT TTTTTTTTTTTTTT TTTT TTTT T TTTTT TTTTTT A A AAAAAAAAAAAA A AAA AAAAAAAA AAAAA AA AAAAAAA A AAAAA AAAA A A AAAA AAA AAAAA AAAAAAAAAA AAAAA AAAAAAAAAAA AAAA AAA A AAGG GGGGGGGGGG G G G G GGG GGGGG GGG GGGGGG G GGG GG GGGG GGG G G G GG G GG G GGGGGG G G GGGGG G G G G G G GGG GGGGGGGG GGGG G GGG G G GGG G G GGG G GGGGGGGG GG GGG GG G GGGGGG G G G GGGG GGGGGG G G G TTT TTT GGG GGG GG GGGGGGGGGGG G GGGG GG GG G G G GGGG G G GGGGGGGG GGGGGG GG G GGGGGGGGGGG GGGGGGGGG GGG G GGAA A A AA A AAA AAA AAAAA AAAAAA AAAA AA AAAAAAAAAAAAAA AAAAAAAA AAAAA A AA A A AAA A A A AAAAAAAAAAAAAAA AA AAAAAAAAAAAAA CCCCCCCCCCC CCCCCCCCCCC CC CCCCCCCC C CCCCCC CCCC CCCCCCCCCCCC CC C CC CCCCCCCCCCCCCC CCCC C CCCC C CCC C CCCCCCCC CCCC T T TTT T T TTTTTTTTT T T T T TT TTTT TT TTTT T T T TTTTT T T TTTTT T TTTT TTTTTTTT TT T T TTTTT TT T TT T TTTTT TTT T TTTT TT TTTTT TTTTTTTTTTT T T TTT TTTTT T TTTTTTT TTTT TTTTTTT T TTT TTTTTT TTTTTTTTTTTTTT T T T TTTT TT TT TTTTTTTT TT TTTTT TTTTT T TTTTTT T T C C CCCCCCCC CCCCCCC TTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTT TTTT T T C CCCCC CC C C C C C C C C C CCC CCCC CC CCC CCCCCCCCCCC C CC CC GGGG GG GT TT TTTT T T TTT T T T A AAAAAAAAAA AAAAAAAAAAAAAAAA AA AAA A AAAAA TT T TTT TT TTTTTTTTTTTTTTTTTTTTTT T TTTTTTTTTT TTTTT TTTTTTT TTT TTTTTTTT TTTT TTTTTTTTTTTT GGGGG GGGGGGGGGGGGGG G GGG GGGGG G GGGGGGG G G GGGGGGGGGGGG G G G GGGGGGGGGGGGG G G G G GG GGGGGGGGG GGGGGGG GGGGGGGGG G GGGGGGGG GGGG G C CC CC C CCCC CCCCCCC CCCCCCCCCCCCCCCC C CC C AAA AAAAA A A AAAAAAAAAAA A AAAAAAAA AAAAA AA AA A AAA AAAAAAAA AA A AAAAAA AAAAAAAAA AA AA AAA AAAA A AA AAAA A AAAA A AAAAAAAAA A AAAA A AAAA AAAA A AAAAAAAA A AAAAAAA A AAAAA A A A AAAA A AAAAAAAAAAAA AAA A AAAAA A AAAAAAAA AAAAA A AAAAAAAAA A AAAAAAA AA A AAAA AA A A A AAAAAAAAAA A AAAAAAAA AAAAAA AAAAAAAA A A A AA AA AAAAA AAAA A AAA AAAAAA A AAAAAAAA AAAAA A A A AA A AAAAA AAAAAA A AA A AAA AA A AAAAAAAAAA A AAAA AAA AAAAAAAAAAAAAAAAAAAAA AAA AA AA A A A A A AAAAA A AAAA AAAAAAA AAAAA AAA A A AAAAA AAAA AAAAAAAAAAAAAAAAAAAA A A A A AAAAA A A AAAA A AAAA AA AA A A AAAA AAAAAAAAAAA A AAAAAAAAAAAAAAA A AAA A AAAAAAAAAAA A AAA A AAA AAAAAAAAAAAAAAAAAAA AAAA A A AA A A AA AAAAA AAAA A A AAAAAAAAAAA AA AA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAA A AAA T TTTTTT T TTT T TTTTT AAAAAAAAA AA AAA A A A AAAAAAAA A AAA A A AA AAAA A AAA AAAAAA A AAA GGGG G GGGGG G G GGGGGGGGGG GGGGG G GG GGGGGGGGGGGG GGGG GGG G GGGGGG G 350 400 450 500 42771000 42772000 42773000 42774000 Time Signal • ~50 (250-400 with new R9 pore) base pairs per second pass through a pore • Need to segment signal into individual events representing base pairs and determine to which base each event corresponds
Nanopore Raw Correction ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ●● ● ● ● ● ●● ● ● ●● ●● ● ● ●● ● ● ● ● ● ● ● ● ●●●● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ●● ● ● ● ● ● ● ● ●● ● ● ●●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ●●● ● ● ● ● ●● ●● ●●●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ●●●● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ●●●● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●●● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●●● ●● ● ● ●● ●● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●●● ● ●●● ● ● ● ● ● ● ●●●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●●● ● 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● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ●●● ● ● ●● ●● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ●● ●● ● ● ●●● ● ● ● ● ● ●● ● ● ● ● ●● ● ●●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ●● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●●● ● ●●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ●● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ●● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● 350 400 450 500 42771000 42772000 42773000 42774000 42775000 Time Signal 50 55 60 65 70 75 42771000 42772000 42773000 42774000 42775000 Start Mean 50 55 60 65 70 75 14200.0 14200.5 14201.0 14201.5 Start Mean GAATT C G G G C T A 42771000 42772000 42773000 42774000 42775000 Start BaseCall A C G T Entropy 0.5 1.0 1.5 SD 0.5 1.0 1.5 2.0 2.5 BaseCall − A C G T Match False True ad6d8bda−1dd5−47be−9898−3bdb250f8b5f Segmentation Call Bases Align to Genome
Nanopore Raw Correction T T TTTTT T T T T T TTTT T T T T T T T T TT T T TT T T T AAA A AA A A AAAA A A AAA A AA C C CCC CCCCCC CC C C C C C C C C C C CCC CCCCC CCCCCC C CC CCCCCCC C C C C C CCCCCC C CCCCC C C CCCCC CC CCC CCC C C C C C C C C C CCC C C C CC C C CCCCCC C C CC C C CC C C C C C C C CC C C C C C CC CC CCC CCC CCCC C C C CC CC C TTTT T T TT TTTTTT T T T GGGG GGGG G GGG GG G G G G G GTT T T T T T TTTT T TT TT T TTT T T A AA A A AA AA A AA AAA AA A A A A AA A A A T TT T T TT TTT TTTTT T TT TTT G G GGGGGG G G G GG G GGG GGG GGG G G G GGG GGGGG G GGG G G GG GGG G G GGG G G G GGGGGG G GG G G G G G G G G G G GG GGG GG GGGG G G GGGGG GG GGG G G G GGG GG G GGGGG GG GG GGGGGGGG G GG G GG GGG G G G G G G G TTT TTTTT T TTTTT TTTTT TT T TTTTTT TTT T T T TT TTTT T T TTTTT TT T TTTT TTTTTTT T T TTTT T T T T TT T TT TTTTTT T TT TT T TTT T TTTTTTTT TTTTTTT T T T T TT T T T T T TT TT T TTTTT TT T T TTTTTTT TTTTTTTT TTT TTT T T T T TT T TT T T TTT T C C C CCCCC CC C CCCCCCCCCCC CC CCC CCC CCCC C CCCCCCCCCC CCCCCCCCCCCCCCCCCCCCCCC CCC C C A A AAA AA AA AA A A A AAAAAA A A AAAAAA A AA A A A A A A A A AAAAAAAAAA A A A AAAA A AAA AA A AAAAAAAA CCCCCC C C C CCCCCCCC CCC CCCCCCC C C CCC CC C C C CCC C C C CCCC C CCC CC C C CCCCCCC C CCCC CC CCCC CC CCCCC C C C C CCC C C C C C C C CC CC CC C C CCCCC CC CC C C C CCC C CC C C C C C CC CCCC C CCC C C CC C CCC C CCCCCCCCC C C C C C CCC CCCC C C CCCCCCC C C CCCCCC CC CC C C CCCC C C CC C CCCCCCC CCC CCCCC C C C CCC C T TTT T TT T TTTTT T TTT T TTTTT TTT T TTTT TTTTTT T T TTT TTTTTTTTTT G G GGGGGGGGGG GGGGG GGGGGGG GGG G G G G G GG G A AAAA A AAAA A AA A A AAAA AAAA A AAAA A A AAAAA A AA AAAA A A AAA A A A A AAAAAAAAAAAA A AA A AA A A A A AA AA A AAA A A A AAA AA AA A A A A AAA A A AA A AAAAA AA A A A AA AA AAA AAAAA AAA AAAAAA AA AAA AAA A A AAA AA AAA AA A AAAAAA AAA AA AA A A A A A A AAAAAAA A A A AAAAAAAAAA A A AA AAAA AAAA A A A A A A AAAA A A A A AAAAAA A A AA AA A A A A A AA A AA A AAAAA A AAAAAA AA A AAA A AA A AAA AAAAAAAAAAAAAAAAA AAAAAAAAAAAAA A T T TT TTT TTTT TTTTTTTT T TTTTTTTT TTTT T T TTTTT T T T TTTTTTTTTTTT T G GG G G G G G G G GG G G GG GG G GGGGGGGGG G G G G GG G G GG GG GG GG G G G GG G G GGGG G G GGGGGGGG G G G GGGG GGG GGGGGG G GGGG TTTT T TTT A AAAAAAAAAA AAAAAAAAA AAA A TT T T T TTTTT T T TTTTTTTTTTTT TTT TTT TT CCCCC C CCCCCC CC CC C C C CC C C C C CCC CCC C C C C C CCCCCCCCCCCC CCC C CCC CCC C C CC C C C C C C CC C C C C C CC C CCCCCC CC CC C CCCCC C CCC C C C C C C C CCCCC C CCCCCCCCCCC C C CCCCCCCC CC C CCCCC C CC CCC C C CCCCC C C CCCCC C CCC C C C C C CCC C C C C CC CCCCCC C CC C C CCCC CC CCCCCCCC CC CCCCCCCCCCCCCC CCCCC CCCC C C C C C CCC C C C C C C CCC CCC C CC CCCCC C CC C CC C C C CCC C C C CC C CC C CC CC C CC C C C C CCC CCCC CCCCCC C CC C C C CC C C CCCCCCC C CC C C C C C CCC C CCCCCC C C CCC C C CCC C C CC C CCC C C C C CCCCCC C CCC CCCCCCCCC C C CCC C C C CCCCCC CCC C C C CC C TTTTTT TTTTTT T TTTTTT TTTTTT TT TTTTTT T TTTTTT T TTTTT T TT T TTTT GGGG G G G GGGGGGGGGGG G GGGGGGGGGGGGGGGGGGG G GG GGGG GGGGG GGGGGGGGGGGGGGGGGG GG GGGGGGG G GG GGGG GGGGGGGGGGGGG G GGG G GGGGGG G GGGGGGG G G GGGGG GGG G G G GGGG G GGGGG C CC C CC CC CCCCC CCC C C CGG G G G G G G G G G GGGGG G G GGGG G G G GG G G GG G GGGGGG G G G G G G GGG GG G G GG G G G G G G G GG G GG G G G G GGG GG G G GG G G G G G G G G GG G G G G G G G G G G G G G G G G G G C C CCC C C C CC C CCCCC CC C CC C CC C C C CC CC C C C C C C C C C C C C CCC C C C C C C C C CC C C CC C CCCC CC C C C C C C CC C C CC A A AA A A AA AA AA A A A A A A AA A A AA AAA A A A A AAA A AA A A A A AAAA A A A A A A A AA A A A A AA A A AA A AA A AA A A A AA A A AA A A AA A A A A AA AAA A AAA AAAAAAA A AA A AA A A A AA AA A A AA A A A A A AA AA AA AAA A A AAA A A AA A AAAAA A AA AA A A A A AAAA A AA A AA AA A AAAAA A AA AAA A A AA AA A A AA A AA A A A A A AAAA AAA AAA A A A A A A A A A A A A A A A A A AA A AAA AA A AAAAA A A A A AA A A A A A A A AAAA A A A A A AA A A A A A A A A A A A A A A A A A AAAA C C C C C C CCC C T TT T T T T T T T TTTTT TTT T TTT T T T T T T T T TTTT T TT T T T TTT TTT T T T T TT T TTTT TT T TT TTT T T TT T TT T T T T T TT T T T TT T T T T T T T TT T T T T TT TTTT C CCC CCC C C C CC C C C C CC C CC C CCCC C DDD D DD DDDDDD D T T TTTTT T TT TT T T T T T T T T T T GGG G GG G GG G G G GGGG GGGGGG GGGGGGG GG GGG GG G G G G GG C C CC C C C CC C C C CCCCCCCC CCCCCC CCC CCCCCCCCC CCCC C CC CC C C CC C C CC C CCCCCCC CCC C C C C C C CCC C CC AA AA A A AA A AA A A A A A AA A A A A AA A A AAAA A A A A A AA AA A A A AA A A A A AA AC C C C C CC C C C C C C CCC C CC C C C C C C C C C C C C C C C T TT T T T T T TT T TT T TT TTT T T T T T TT TT T TT T T T TT T TT T T T T T T T TT T T T T T T T T T TTT T TT T T T T T T T T T D D DDD D D D D D D D DDDD D DD D DD D D D D D DD D D D D D DD DDD D D D G G GG GGG G G G C CCC C CC C CCCC CC C CC C CC C GGGGGGGGGG G GGGGGGGGG GGG G D DDD D DDD DD T T T TTT T T TT T TTTT TTT G G GGGG AAAA A AAAAAAAAAAAA A AAAAAAAAAAAAA AAAAA A AAAAAA AAAAA AA AAAAAAAAA GG GGGG GGGGGGGGGGGGGGGGGG C CCCCC CCCC C C C C TT TT TTTTT TTT TTTTTT TTTTTT GG G G G GG G GGGGGGG G GTTT T T TT T T TTT TTTTTT T T TTTT TTT TTT T T TTTT T TTTTT T TTT T T GGGGG G G G GGG GG G G G GG G GG T TT T TT TTTT TTTTTT T TTTTTTTT TTTTTTTTTT T TTTT T T T C C CC C C CCCC C CC C CCC C C C CCCC C CCCCCCC C CCCC C C C CCCCC CCCCCCCC CC C C CCCCCC C CCCCCCCC CC C CCCCC CCCCCC CCCCCCCC CC CCC C C C CC C CC AAAAAAAAAAAAA CC C CCCCC C C CCCCCCCC CCCCCCC C CC CC CC CC CCC T T T T T TT T T TT TTTTT T T A A AA AAA A A A A C C CC C C CCC C C C CT T T T TTTTTT T T T T TTT T T TT T TT T T T T T T G GG G G GGG GGGG G G G G G GGGG G G G G G G G GG GG G G G GGG T T TT T T TTT TT TTTT T T T T T T TT TT T T TT T T TTTTT TTT T T T T T T T TTT T TTTTT TT T TT TT T TTTTTTTT T TT T TT T T T T T T TTTT TT TTTTTTT T T T TT TT TTT T T GGGGGG G GGGGGGA AA A AA A AA A A A A AAAA AA AAAAAAA A AAA AA A A A AA A AAAA AAAAA AA AAA A T T TTT T T T TTT TTTTT T T T TTT T TTTTT TT TTT T TTTTTTTTT TTTTT TTTTTTTT TTTTTTTTTTTTTTTTTTTTT G CCT AA AAG C GCTC300 350 400 450 500 550 107161000 107162000 107163000 107164000 Time Signal T TTTTTT TTTTTTTTTT T TTTT T TTT TTTTT T T AAA A AAA AAAAAA A AAA A AAC CCCC CCCCCC CC C C C C C CC C CC CCC CCCCC CCCCCC C CCCCCCCCC C CC C C CCCCCC C CCCCC C C CCCCCCCCCCCCC C C C C C C C C CCCC C C C CCCC CCCCCC C C CC C C CCC C C C C CCCCC CCCCCCCCCCC CCCCCCCC CC CCCCC TTTT T T TT TTTTTT T T T GGGGGGGG G GGG GG G G G G G GTT T T T TTTTTT T TTTTT TTTT T A AAAA AAAAA AA AAAAAAAAAAA A AATTT T TTTTTTTTTTTTTT TTTG G GGGGGG GG GGG GGGGGGGGGGGG G GGGGGGGG G GGG G G GG GGG G G GGG G G GGGGGGGGGG G G G G G G G G G G GG GGG GG GGGG GG GGGGG GG GGG G G G GGG GG G GGGGGGG GG GGGGGGGG G GG G GG GGG G G G G G G G TTT TTTTT T TTTTT TTTTT TTT TTTTTT TTT T T T TT TTTT T T TTTTT TT T TTTT TTTTTTT T T TTTT T T T T TT T TT TTTTTT T TT TT T TTT T TTTTTTTT TTTTTTT T T T T TT T T T T T TT TT T TTTTT TT T T TTTTTTT TTTTTTTT TTT TTT T T T T TT T TT G G GGGG C C C C C CCC CC C CCCCCCCCCCC CC CCC CCC CCCC C CCCCCCC CCC CCCCCCCCCCCCCCCCCCCC CCC CCC C C AA AAA AA AA AA A A A AAAAAAA AAAAAAA A AAA A A A A A AAAAAAAAAAAA A A A AAAA AAAAAA AAAAAAAAA CCCCCC C CC CCCCCCCCCCC CCCCCCCC CCCCCCCCCCCCC C C CCCC C CCCCCCC CCCCCCCCCCCC CCCCCCCCCCCCC C CC C CCC C CCC C C C CCCCCCC CCCCCCCCCCC C C CCC C CCCC C C C CCCCCC C CCC C C CCC CCC CCCCCCCCCC C C C C CCCCCCCCC C CCCCCCCC C CCCCCCCCCCC C CCCCCC CC CCCCCCCC CCCCCCCC C CCCCC C T TTT T TT T TTTTT T TTTT TTTTT TTT T TTTT TTTTTT T T TTT TTTTTTTTTT G G GGGGGGGGGG GGGGG GGGGGGG GGG C C C C C CC C TTTTT T TTTT TTT TTTTTT TTTTTTTTT T T TTTTT T TTTTTT T T TTT T T T T TTTTTTTTTTTTT TT TTTT T T T TTTT TTTT T T TTTT TT TT T T T T TTT T T TTTTTTTTTT T T T TTTTTTTTTTTTTTTTTTTTT TTTTT TTT T T TTT TTTTTTT T TTTTTTTTTTTTTT T TTT T TTTTTTTTT T TTTTTTTTTTTTTT TTTTTTTTT TTT T T TTTT T T T T TTTTTTT T TTTT TTT TTTTT TT T TTTTT TTTTTTT TT TAAA A AA A AAAAA AAA AAAAAAAAAAA A AAAAAA AAAAAAA A TT TT TTT TTTTTTTTTTTT T TTTTTTTT TTTTT TTTTTT T T T TTTTTTTTTTTT T GGGGGG G G G G GG G GGG GG GGGGGGGGGG G G G GGG G GGG GG GG GG G G G GGG G GGGG G G GGGGG GGG G G G GGGG G GG GGGGGG G GGGG TTTT T TTT A AAAAAAAAAA AAAAAAAAA AAA A AA A A A AAAAA A A AAAAAAAAAAAA AAA AAA AA TTTTT T TTTTTT TTTTT TT TT T T T TTTT TTT T TT T TTTTTTTTTTTTTTTTTTTTTTTTTTT TT T T T TTTTTT T T TT AAAAAAAAA AA AAAAAAAAAAA AAA A A A AAAAAAAAAAAAAAAAA A A AAAAAAAA AA A AAAAA AAAAAAAAAAAAAA AAAAAA AAAA A AAA AAAA A AA AAAAAAAAAA AA A AAAAAAA AAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAA AA AAAA A A A A AAAAAAA A AA AAAAA AAA AAA A A A AAA A A AAA AAA A AA AA A AA A AA A AAA AAAAAAAAAA AAA A A A AA A A AAAAAAAAAA A A AA AAAA AAAAAAA A A AAA AAAAAA A AA A AAA A A A AAAAAAA AAAAAAAAAAAAA AA AAA A A A AAAAAAAAA CC C CC C T TTTT T T TTTTT T TTTT T T TTTTTT TT TTTTTT T TTTTTT T TTTTT T TT T TTTT GGGG G G G GGGGGGGGGGG G GGGGGGGGGGGG GGGGGGG G GG GGGG GGGGG GGGGGG GGGGG G GGGGGG GG GG G GGGG G GG GGGG GGGGG GGGGGGGG G GGG G GGGG GG G GGGGGGG G G G GGGG GGG G G G GGGG G GGGGG C CC C CC CAAAAAA AAA A AAAAAAA AAA A AAAAAGGG G GGGGG G GGGG GGGGGGGGGGG G G G GGGGG GGG G GGGG GGGG G GGGGG GGG GGGGGGG G GGGG GG GG GG GG GG G G G G GG GGGGG G G G G G C C CCC C CC CCCCCCCCCCCCCCCCC C C CCCCCCC C C CC CC C C CCCC C CC C CCC C CCC C CCCCCCCCC C C CC CCCCCC CC AAAA AA AA AA AA A AA AA A AA A AAAAAA A AA A AAA A AA A A AAAAAAAAA A A AAAA A AAA AAAAAA A AA A AA A AAAAA AAAA AAA A AA AAAAAA AAAAAAAAAAAAAAAAAAA A AAAA A A AAA A A AA AAAAAAAAAAAAAA AAAAAAAAAA AAAAA A A AAAAAAAAA AAA AAAAAAAA A AAAAAAAAAAAA A AAAAA A A A A A AAAAAAAAAA AAAAA AAA A AA A AAAAA AAA AAAAAAAAAAA A A AA AA AAAAA A A AAAAA AAA AAA A AAA A AA A A AAAA A A AAAAAA CC CC C CCCCC TTTT T T TTTTTTTTTTTT T TTT T TT TT TT T TTTT TTT T T T TTTTTTT T TT TTTTTTTTTT TTTTTTTTT T TT TTTTTTTTTTTTT TTT T T T TT TTT T TTTTTT CCCC CCCCC C CCCC CCCTTTT T TTTTG GGG G GG GGGGGG C C C CCCCCC CCCC C CC CC CC CC C GGG G GG G GGG G G GGGG GGGGGGGGGGGGG GG GGGGGG G G G GG C C CC CC C CCC CC CCCCCCCCCCCCCC CCCCCCCCCCCCCCCC C CC CC CCCCCC CCCCCCCCCCCCC C C C C C C CCCCCC AAAA A A AAAAAAAAA AAAA A AAAAAAAAAA A AAAAAAAAAAAAAAA AAAAAC C C C CCCC CC CCCCCCCCCC CC C C CC C C CCCC CC T TTTTTT TTT T TT TTTTTTTT TTTTTTTTTTT TTTT T TT TTTT TT T TTTTT TT TT T TTTT T TT TTT T TTT T T TT TTTTTT T T TTTTTT TTT T TTT T T T T TT TT TTT TTTTTTTT T T GG GGG G G G C CCC C CCC CCCCCCCCCC CC C GGGGGGGGGG G GGGGGGGGG GG G G G G GG G GGG GG T T T T TT T T TT T TT TT TTT G G GG G G AAAA A A AAAAAAA AA A A A AAAAAAAAAA AA A AAAAA A AA AA AA AAAAA A A A AAAAAAAA GG GGGG GG GG GGGGGGGGGG GG GG C CCCCCCCCCC C C CTT TT TTTTT TTT TTTTTT TTTTTT GG G G G GG G GGGGGGG G G TTT T TTT T TTTT TTTTTT T T TTTT TTT TTT T T TTTTTTTTTT T TTT T TGGGGG GGGGGGGGGG GGGG GG TTT T TT TTTT TTTTTT T TTTTTTTT TTTTTTTTTT T TTTT T T T C C CC C C CCCC C CC C CCC C C C CCCC C CCCCCCC C CCCC C C C CCCCC CCCCCCCC CC C C CCCCCC C CCCCCCCC CC C CCCCC CCCCCC CCCCCCCC CC CCC C C C CC C CC AAAAAAAAAAAAA GG G GG GGG C C C CCCCCCC CCCCCCC C C C C C CT TT TTT TT T T T TT T TTT TTTTT TT A AAAAAA A A AA CC CCCC CCCC C C CC C C CCCCCCCC C C CCCC C C CC CCCT TTT T T GGG G GGGGGGGG G G G G GGGGG G GG GG GG GGGGG G G GGG T TTT T TTTT TTTTTTTT TTTTTTTT T TTTT T TTTTT TTTTTT T T T TTTT T TTTTT TT TTTTT T TTTTTTTT T TT T TT T T T T T T TTTT TT TTTTTTT T T T TT TT TTT T T GGG GG G G G GGGGGA AA A AA AAA A AA A AAAA AA AAAAAAA A AAA AA A A A AA A AAAA AAAAA AA AAA A T T TTT T T T TTT TTTTT T T T TTT T TTTTT TT TTT T TTTTTT T TT TTT TT TTTTTTT T TTTTTT TTTTT T TTTTTTTTT 350 400 450 500 550 107161000 107162000 107163000 107164000 Time Signal
Nanopore Raw Correction T T T TT T TT TT T TT T TT T TT TT T T T T TT T T TTTTTTTTT TT TT T T T T T T TT T T T T C C C C C CCC CCC CCC C CCCC C CCCCCCC C CCCC C CCC C C T TT T TTT TTT TTTT T TTT T T TT TTT TTTT TTTTTTT T TTT T T TTTTT T T TT T T T TT TTTT TTTTT TTT T T T TT TTTTTT T T T T T TT G GGG GG GGGG GGG G GG GGGGGG GG GGG GGGGG GG TTTTT T T TTTTTTTTTT TTT T T T TTTT T TTTTT T TT TTT T TTT T T TTTTTT T TT TTT T T T TT CC C CCCC CCCCCCCCC CC GG GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG GGGGG GGGG GG GGGGGGGGGGGGGG G G G GGGGG G GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG GGGGGGGGGGGGG G GGGGGGGGG G GGGG G GGG G GGGDDDDDDDDD DDDDDD DDDDD D DDDDDDDD DDDDDDDDD D DDDDDDDDDDDDD DDDDDDDDDDDD DDDDDDDDDD DDDDDDDDDDDDDDDDDDDD D DDDDDDDDDDDDDDDDDDDDDDDDDD D DDDDDDDDDDDD DDDDDDDDDD D DDDDDDDDDDDDDDD D D DDD DDDDDDDDDDDDDDDD DD DD D DDD D DDDD C CC CC CCC CC CCC C CCCCC C C AA AAAAAAA AAAAA A A A A AA A AA AA AAAAA AAAAAAAAAAAAA AAA AGGG G G G GGG GG GG G G GGGG G G G G G G G GGG G G G G G G G GG G GGG GG GGGG G GGG GGG G G G GG GG CC CCC C C C CCC C C C C C C C C C C C C C C C C CC CC C C CC C CCCC C C C C C C C C C C C C CC C C CCC C CC C CC C C C C CC C CCC CC CC C C CCC CC CC C C CCC C C CC C C C CCC C C C CC C C C C CC CCCCCC C CCCCC C CCC C C C CCCCCCCCCCC C C C CCCC CCCCC C C CC CCCCCC CC CC C C CCCC C CCC C C C C C CCCCCC A A A A A A A A A A A A A AA A A A TTT T TTTTT T TTT TTTT TT T T T G G G G GGGGG GG GGG A A A AA AA A A AAA AA AAA A A AA A A A A A AA A A A AA A A A A A A A A A A AA A TT TT T TTTT T TT T T TT TT T T T TT T T TT T T T 23604000 Time T TTTTTT T TT T TTTTTTT T TTT TTT TTTT T TTTTTT TTTTTTTTTTTTTT T TT T TTTTT TTT C CC C CCCCCCC CCCCCCCCCCCCCCCCCCCCCCCCC CC T TT T TTT TTTTTTTTTTTT T TTTTTTTTT TTTTTTT T TTTT T TTTTTT T TT T T T TT TTTTTTTTTTTTTT T TTTTTTTTTTTTTTT GGGGGGGGGGGGGGGGGGGGGGGG GGG GGGGG GG TTTTT T TTTTTTTTTTTTTT T T TTTTTT TTTTT T TT TTTT TTTTTTTTTTTTTTTTTT T TTT CCC CCCCCCCCCCCCC CC GG GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG GGGGG GGGG GG GGGGGGGGGGGGGG G G G GGGGG G GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG GGGGGGGGGGGGG G GGGGGGGGG G GGGG G GGG G GGGGGGGGGGGGGGGGGGGGGGG G GGGGGGGG GGGGGGGGG GGGGGGGGGGGGGG GGGGGGGGGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGGGGG G GGGGGGGGGGGGGGGGGGGGGGGGGG G GGGGGGGGGGGG GGGGGGGGGG G GGGGGGGGGGGGGGG G GGGG GGGGGGGGGGGGGGGG GGGG G GGG G GGGG CCC CC CCCCCCCCC CCCCCCC AAAAAAAAA AAAAAA AA A AAA AA AAAAAAAAAAAAAAAAAAAAAAA AGGG GG G GGGGG GGGGGGGG G G G G G G GGGGG G GG G G GGGG GGGGGGGGGGGGGGGGG GG GG GG CCCCCC CC CCC C C C C C C C C C C C C C C C CCC CCCCCCC CCCC C C C C C C C CC C C CCC CC CCC C CC C CC C C CC CC C CCCCC CC CC CCC CC CC C C CCC C C CCC C C CCC C C C CC C CC C CC CCCCCC C CCCCC C CCCC C C CCCCCCCCCCCCCC CCCC CCCCCC CCCCCCCCCCCCC CC CCCC CCCCCC C C CCCCCCC AA AAAAAAAAAAAAAAAA TTTT TTTTT T TTTTTTTTT T T T G GG G GGGGG GG GGG AAAAAAAA A AAA AA AAAA AAA A A A A A AA A A AAA A A A AA A A A A A AAA TTTTT TTTTTTT TTTTTTTTTTTTTTTT T TTTTTTTTT 23604000 T T T TT T TT TT T TT T TT T TT TT T T T T TT T T TTTTTTTTT TT TT T T T T T T TT T T T T C C C C C CCC CCC CCC C CCCC C CCCCCCC C CCCC C CCC C C T TT T TTT TTT TTTT T TTT T T TT TTT TTTT TTTTTTT T TTT T T TTTTT T T TT T T T TT TTTT TTTTT TTT T T T TT TTTTTT T T T T T TT G GGG GG GGGG GGG G GG GGGGGG GG GGG GGGGG GG TTTTT T T TTTTTTTTTT TTT T T T TTTT T TTTTT T TT TTT T TTT T T TTTTTT T TT TTT T T T TT CC C CCCC CCCCCCCCC CC GG GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG GGGGGG GGGGGGGGGGGGGG G G G GGGGG G GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG GGGGGGGGGGGGG G GGGGGGGGG GGGGG G GGG G GGGDDDDDDDDD DDDDDD DDDDD D DDDDDDDD DDDDDDDDD D DDDDDDDDDDDDD DDDDDDDDDDDD DDDDDDDDDD DDDDDDDDDDDDDDDDDDDD D DDDDDDDDDDDDDDDDDDDDDDDDDD D DDDDDDDDDDDD DDDDDDDDDD D DDDDDDDDDDDDDDD D D DDD DDDDDDDDDDDDDDDD DD DD D DDD D DDDD C CC CC CCC CC CCC C CCCCC C C AA AAAAAAA AAAAA A A A A AA A AA AA AAAAA AAAAAAAAAAAAA AAA AGGG G G G GGG GG GG G G GGGG G G G G G G G GGG G G G G G G G GG G GGG GG GGGG G GGG GGG G G G GG GG CC CCC C C C CCC C C C C C C C C C C C C C C C C CC CC C C CC C CCCC C C C C C C C C C C C C CC C C CCC C CC C CC C C C C CC C CCC CC CC C C CCC CC CC C C CCC C C CC C C C CCC C C C CC C C C C CC CCCCCC C CCCCC C CCC C C C CCCCCCCCCCC C C C CCCC CCCCC C C CC CCCCCC CC CC C C CCCC C CCC C C C C C CCCCCC A A A A A A A A A A A A A AA A A A TTT T TTTTT T TTT TTTT TT T T T G G G G GGGGG GG GGG A A A AA AA A A AAA AA AAA A A AA A A A A A AA A A A AA A A A A A A A A A A AA A TT TT T TTTT T TT T T TT TT T T T TT T T TT T T T 23604000 Time T TTTTTT T TT T TTTTTTT T TTT TTT TTTT T TTTTTT TTTTTTTTTTTTTT T TT T TTTTT TTT C CC C CCCCCCC CCCCCCCCCCCCCCCCCCCCCCCCC CC T TT T TTT TTTTTTTTTTTT T TTTTTTTTT TTTTTTT T TTTT T TTTTTT T TT T T T TT TTTTTTTTTTTTTT T TTTTTTTTTTTTTTT GGGGGGGGGGGGGGGGGGGGGGGG GGG GGGGG GG TTTTT T TTTTTTTTTTTTTT T T TTTTTT TTTTT T TT TTTT TTTTTTTTTTTTTTTTTT T TTT CCC CCCCCCCCCCCCC CC GG GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG GGGGG GGGG GG GGGGGGGGGGGGGG G G G GGGGG G GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG GGGGGGGGGGGGG G GGGGGGGGG G GGGG G GGG G GGGGGGGGGGGG GGGGGGGGGGG G GGGGGGGG GGGGGGGGG G GGGGGGGGGGGGG GGGGGGGGGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGGGGG G GGGGGGGGGGGGGGGGGGGGGGGGGG G GGGGGGGGGGGG GGGGGGGGGG G GGGGGGGGGGGGGGG G GGGG GGGGGGGGGGGGGGGG GGGG G GGG G GGGG CCC CC CCCCCCCCC CCCCCCC AAAAAAAAA AAAAAA AA A AAA AA AAAAAAAAAAAAAAAAAAAAAAA AGGG GG G GGGGG GGGGGGGG G G G G G G GGGGG G GG G G GGGG GGGGGGGGGGGGGGGGG GG GG GG CCCCCC CC CCC C C C C C C C C C C C C C C C CCC CCCCCCC CCCC C C C C C C C CC C C CCC CC CCC C CC C CC C C CC CC C CCCCC CC CC CCC CC CC C C CCC C C CCC C C CCC C C C CC C CC C CC CCCCCC C CCCCC C CCCC C C CCCCCCCCCCCCCC CCCC CCCCCC CCCCCCCCCCCCC CC CCCC CCCCCC C C CCCCCCC AA AAAAAAAAAAAAAAAA TTTT TTTTT T TTTTTTTTT T T T G GG G GGGGG GG GGG AAAAAAAA A AAA AA AAAA AAA A A A A A AA A A AAA A A A AA A A A A A AAA TTTTT TTTTTTT TTTTTTTTTTTTTTTT T TTTTTTTTT 23604000 1. Center on deletion 2. Expand to neighboring regions 3. Segment using mean changepoint Correct deletions:
Nanopore Raw Correction 1. Center on insertion 2. Expand to neighboring regions 3. Segment using mean changepoint Correct insertions : CCC CCCC C CG G G GG GGG G GG G GG GGG G GGG GG G G G GGG GGGG G G G GGGG GG G G G GGG G G G G G G GG G G G G G GGGG G G G C CC CCCCCCCCCC CCCCC C C CCCCCCC C CCCCCCCCC CCCCCC CC A AAAAAAA A AG GGGGGGG G GGGG CCCCC C CCCCCCCCCCCCCCCCCCCCCC CCCC CCCC CCCCCCCCCCCC C CCCCCC CCCCCCCC CTT T T TTTTTTTTT T TT TTT TTTTTTTT TTT TTT TTTT TTT T TTTTT T TTTTTTTTTTT TT TTTTTTT TTTTTTTT TT T T TTT TTTTT TTTTTTTT T T GGGGGG GGGGGGGGGG GGGGGGGG G GG GG G G GGGGG GGGG GGGGGGGGGG G GG GG G GGGG G GGGGG G GGGGGG GG G G G G GG GGGGGG GGGG G GGGGGGGGGGGG G G GGG G G GGGG G GG GGGGGGGGGGGGGGGG G GGGG GGGGGG GGGGGGGGGGGGGGGGGG GGG GGGGG G G GG GGGGG G G G GGGGGGGGGGGG GGGGGGGGGGGGGGGG G GGGGGGGGGG GGGGGGGGGGG GG G GG GGGG G GGG G GGGGGGGGGGG G G GGGGG GGGGGGGGGGG GGGGGGGGG GG GGGGG GGGGGG GGG GGGGG GGGG GGGGG G GGGGG GGGGGGGGG GGGGGGGGGG GGGG GG GGG GG GGGGGGGGGGG G GG GG G GG GG G GG GGGG GGG GG GG GGGGGGGGG G G G GGGGGGGGG G GG G G G GG G G G G GG GGGGGG G GG GGG G G GG G GG GG G GG G G GGG G G GG C CCCCCC CCCCCCC C A AAA AAAA AAA AA AAA A T TTTTTTTTTTTTTTT TTTT T TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT TTTTTTTT AAAA AAAAAAAAAAAA AAAAAAAAAAAAAAA CCCCC C CCC CCCCCCCCCCC CCCCCCC CCC CCCCCCCCCCC CC CCCTTTTTTTTT TTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTT TT T G GGGGGG GGGG DDDDDDDDDD DDDDDDD DDDD D DDDD DD D DD D D G GG GGGG GG GG CC C CC CCCCCC CCCC CCCC A A AA A A A A A AA A A AA A A A A A AA AAAA A A AAA AAA A AA A AA AA AA AA A AA A A A AAAA A A AAAAAAAAAA CCCCC CCCCCCCC C C C CCCCCCC C C CCCCCCC CCCCCC C CCC CC C CCCC GGGGGGG T 6523000 4652400 CCC C C CG G G GGGGG G GG G GGGGGGGGG GG GG G GGGGGGG GGG GGGG GG G G G GGG G G G G G GGG GG G G G GGGGGG G C CC CCC CCCCCCC CCCCC C C CCCCCCC C CCCCCCCCC CCCCCC CC A AAAAAAA A AG GGGGGGG G GGGG CCCCC C CCCCCCCCCCCC CCCCCCCCC C C CCC CCCC CCCCCCCCCCCC C CCC CCC CCCCCCCC C TTT T TTTTTTTTTT TTTTT TTTTTTTT TTT TTT TTTTTTT T TTTTT TTTTTTTTTTTT TT TTTTTTTTTTTTTTTTTT T TTT TTTTT TTTTTTTT T T GGGGG G GGGGGGGGG G GGGGG G GG G GG GG G G GGGG G GGGG GGGGGGGGG G G G G GG G GGGG G GGGGG G GGGGGG GG G G G G GG GGGGGG TTTT T TTTTTTTTTTTT T T TTT T T GGGG G GG GGGGGGGGGGGGGGGG G GGGG GGGGGG GGGGGGGGGGGGGGGGGG GGG GGGGG G G GG GGGGG G G G GGGGGGGGGGGG GGGGGGGGGGGGGGGG G G GGGGGGGGG GGGGGGGGGGG GG G GG GGGG G GGG G GGGGGGGGGGG G G GGGGG GGGGGGGGGGG GGGGGGGGG GG GGGGG GGGGGG GGG GGGGG GGGG GGGGG G GGGGG GGGGGGGGG GGGGGGGGGG GGGG GG GGG GG GGGGGGGGGGG G GG GG G GG GG G GG GGGG GGG GG GG GGGGGGGGG G G G GGGGGGGGG G GG G G G GG G GG G GG GGGGGGGGG GGG G G GG GGGGG G GG G G GGG G G GG C CCCCCC CCCCCCC C A AAA AAAA AAA AA AAA AT TTTTTTT TTTTTTT T T TTT T T TTT TTTTTTTT TTTT TTTTTT TTTTT T TTTTTTTTTT T TTTTTTTT TTTTTTTTTTTTTTTTTTT TTTTTTTT TT T TT TTTTTTTT AAAA A AAAA AAAAAA A AAAAAAAAAAAAAAA CCCCC C CCC CCCCCCCCCCC CCCCCCC CCC CC C CCCCCCC C CC C CCTTTTTTTT T TTTTTTTTTTT TTTTTTTTT T TT T TTTT TT T TTTTTTTT T TT T G GGGGGG GGGG GGGGGGGGGG GGGGGGG GGGG G GGGG GG G GG G G G GG GGGGGG GG C C C CC CCCCCC CCCC CCCC A A AA A A AAAAA A A AA A AAAAAAAAAAAA AAA AAA A AA A AA AA AA AAA AAA A A AAAA A A AAAAAAAAAA CCCCCCCCCCCCCCC C CCCCCCC CCCCCCCCCCCCCCCC CCCCC C CCCC GGGGGGG 6523000 4652400 CCC CCCC C CG G G GG GGG G GG G GG GGG G GGG GG G G G GGG GGGG G G G GGGG GG G G G GGG G G G G G G GG G G G G G GGGG G G G C CC CCCCCCCCCC CCCCC C C CCCCCCC C CCCCCCCCC CCCCCC CC A AAAAAAA A AG GGGGGGG G GGGG CCCCC C CCCCCCCCCCCCCCCCCCCCCC CCCC CCCC CCCCCCCCCCCC C CCCCCC CCCCCCCC CTT T T TTTTTTTTT T TT TTT TTTTTTTT TTT TTT TTTT TTT T TTTTT T TTTTTTTTTTT TT TTTTTTT TTTTTTTT TT T T TTT TTTTT TTTTTTTT T T GGGGGG GGGGGGGGGG GGGGGGGG G GG GG G G GGGGG GGGG GGGGGGGGGG G GG GG G GGGG G GGGGG G GGGGGG GG G G G G GG GGGGGG GGGG G GGGGGGGGGGGG G G GGGGG GGGG G GG GGGGGGGGGGGGGGGG G GGGG GGGGGG GGGGGGGGGGGGGGGGGG GGG GGGGG G G GG GGGGG G G G GGGGGGGGGGGG GGGGGGGGGGGGGGGG G G GGGGGGGGG GGGGGGGGGGG GG G GG GGGG G GGG G GGGGGGGGGGG G G GGGGG GGGGGGGGGGG GGGGGGGGG GG GGGGG GGGGGG GGG GGGGG GGGG GGGGG G GGGGG GGGGGGGGG GGGGGGGGGG GGGG GG GGG GG GGGGGGGGGGG G GG GG G GG GG G GG GGGG GGG GG GG GGGGGGGGG G G G GGGGGGGGG G GG G G G GG G G G G GG GGGGGG G GG GGG G G GG G GG GG G GG G G GGG G G GG C CCCCCC CCCCCCC C A AAA AAAA AAA AA AAA A T TTTTTTTTTTTTTTT TTTT T TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT TTTTTTTT AAAA AAAAAAAAAAAA AAAAAAAAAAAAAAA CCCCC C CCC CCCCCCCCCCC CCCCCCC CCC CCCCCCCCCCC CC CCCTTTTTTTTT TTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTT TT T G GGGGGG GGGG DDDDDDDDDD DDDDDDD DDDD D DDDD DD D DD D D G GG GGGG GG GG CC C CC CCCCCC CCCC CCCC A A AA A A A A A AA A A AA A A A A A AA AAAA A A AAA AAA A AA A AA AA AA AA A AA A A A AAAA A A AAAAAAAAAA CCCCC CCCCCCCC C C C CCCCCCC C C CCCCCCC CCCCCC C CCC CC C CCCC GGGGGGG T 6523000 4652400 CCC C C CG G G GGGGG G GG G GGGGGGGGG GG GG G GGGGGGG GGG GGGG GG G G G GGG G G G G G GGG GG G G G GGGGGG G C CC CCC CCCCCCC CCCCC C C CCCCCCC C CCCCCCCCC CCCCCC CC A AAAAAAA A AG GGGGGGG G GGGG CCCCC C CCCCCCCCCCCC CCCCCCCCC C C CCC CCCC CCCCCCCCCCCC C CCC CCC CCCCCCCC C TTT T TTTTTTTTTT TTTTT TTTTTTTT TTT TTT TTTTTTT T TTTTT TTTTTTTTTTTT TT TTTTTTTTTTTTTTTTTT T TTT TTTTT TTTTTTTT T T GGGGG G GGGGGGGGG G GGGGG G GG G GG GG G G GGGG G GGGG GGGGGGGGG G G G G GG G GGGG G GGGGG G GGGGGG GG G G G G GG GGGGGG TTTT T TTTTTTTTTTTT T T TTT T T GGGG G GG GGGGGGGGGGGGGGGG G GGGG GGGGGG GGGGGGGGGGGGGGGGGG GGG GGGGG G G GG GGGGG G G G GGGGGGGGGGGG GGGGGGGGGGGGGGGG G G GGGGGGGGG GGGGGGGGGGG GG G GG GGGG G GGG G GGGGGGGGGGG G G GGGGG GGGGGGGGGGG GGGGGGGGG GG GGGGG GGGGGG GGG GGGGG GGGG GGGGG G GGGGG GGGGGGGGG GGGGGGGGGG GGGG GG GGG GG GGGGGGGGGGG G GG GG G GG GG G GG GGGG GGG GG GG GGGGGGGGG G G G GGGGGGGGG G GG G G G GG G GG G GG GGGGGGGGG GGG G G GG GGGGG G GG G G GGG G G GG C CCCCCC CCCCCCC C A AAA AAAA AAA AA AAA AT TTTTTTT TTTTTTT T T TTT T T TTT TTTTTTTT TTTT TTTTTT TTTTT T TTTTTTTTTT T TTTTTTTT TTTTTTTTTTTTTTTTTTT TTTTTTTT TT T TT TTTTTTTT AAAA A AAAA AAAAAA A AAAAAAAAAAAAAAA CCCCC C CCC CCCCCCCCCCC CCCCCCC CCC CC C CCCCCCC C CC C CCTTTTTTTT T TTTTTTTTTTT TTTTTTTTT T TT T TTTT TT T TTTTTTTT T TT T G GGGGGG GGGG GGGGGGGGGG GGGGGGG GGGG G GGGG GG G GG G G G GG GGGGGG GG C C C CC CCCCCC CCCC CCCC A A AA A A AAAAA A A AA A AAAAAAAAAAAA AAA AAA A AA A AA AA AA AAA AAA A A AAAA A A AAAAAAAAAA CCCCCCCCCCCCCCC C CCCCCCC CCCCCCCCCCCCCCCC CCCCC C CCCC GGGGGGG 6523000 4652400
Nanopore Raw Correction Complex Corrections : TT CCCCCCCCCCC CCCCCCCC C C C CCC CCCCCCCC CCCC AAAA AAAAAAA AAAAAAAAAA AAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAA AAAAAAAA A A TTTTTTTTT TTTTTTT TTTT T TTT TTT TTTT TTT T TTTT TTTTT TTTTT T T TTT T TTT T TTTTTTT T TT T T TTTTTTTTTTTTTTT T TT T TTTTTTT TTTT TTTTT G GGGG G GGGGG GGGG GGG G GGGGG GGGG G G GGGGG G T TTTTT TTTT T TTTT T T T TT TT T TTT TTTT T T T T T TTT TTTTT TT T T T T TT TT T T T T TT TTT C CC C CCCCCCCCCCCCCCCCCCCC CCCCCCCC AAAAAAAAAA AAA A G GGGGGGGGGGGGGGGGGGGGGGGG G G GGGGGGGGGG GGGGGGGGG GG GGGG GGG G GGGGGG GGGGG G GGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGGGG G GGGGGGGGGGGG GGGGGG G G CCCCCCCC C C CCCCCCCCCC CCCCCCC C CCCCCCCCC C CCCCCCCCCC CC C CCCCCCCCCCC C CCC CCCCCCCC CCCCCCC CC CCCCCCCCC CCC CCCCC C CCCC C CCCCCCCCCC CC CCCCC CT TT TTTTTTTTTTTTTTTTTTTTT D DD DDDDDDDD DDDDDDDDDDDDDDDDDDDDDDD DDD D DDDDDDDDDDDDDDDDDDDDDDA AAAAAA AAAAC CCCCCC C CCCCCCC C CCCCCCCCCC CCC C C CCCC C CCCCC C CC CCC C T T TT T T T T T T T T T TTT T T TT T T T T T T T T T T TT TT TT TT T TTTTT T T T T T T T TTT TT TTT TT T T T T T T T TTTTTT T T T T T T C C CC CCCCCC CCC C C CCCCC C CC CC C CCC CCC C CCCCC C CC CC CC CC CC C C T T TT TT TTT TT T T TTT T TTT T T TT T TT TT T T TTTTT T T TT T T T TT T TTT TT T T TT TTT TTT TTTTTTTTTT TTTT C CC CC CCCCCCCCC C C C CCC CCCCCCCC CCCCCC CCC C CCCCC CCCC AA A AAAAAAA AAAAAAA AAAA A AAAAAA A AAA AA A AAAAAAAA A A AAAAAAA A AA AAAA A A A AAAAAA AAAAAA G 00 46526000 TT CCCCCCCCCCC CCCCCCCC C C C CCC CCCCCCCC CCCC AAAA AAAAAAA AAAAAAAAA A AAAAAAAAAAAA AA AAAA AAAAA A AAAA AAA A AAAA AAA A A A TTTTTTTTT TTTTTTT TTTT TTTTTTTTTTT TTT T TTTTTTTTTTTTTTT T TTT T TTT T TTTTTTT T TTT T TTTTTTTTTTTTTTT T TTTTTTTTTTTTTT TTTTT G GGGG G GGGGG GGGG GGG G GGGGGGGGGG G GGGGG G T TTTTTTTTT TTTTT T T T TT TT T TTT TTTTT T T TTTTTTTTTTTTTT T TTT TT T TT T TTTTT C CC C CCCCCCCCCCCCCCCCCCCCCCCCCCCC AAAAAAAAAA AAA A G GGGGGGG GGGGGGGGGGGGG GGGG G G GGGGGGGGGG GGGG GGGGG GG GGGG GGG G GGGGGG GGGGG G GGGGGGG G GGG GGG G GGGG GGGGG GG GGGGGGG GGGGGGGGGGGGG GGG GGG G GGGGGG GGGGGG G GGGGG G G G GGGGGGG G G GGGG GGGGGG GGGGGGG G GGGGGGGG G G G G G GGGGGGG GG G GGG GGGGGGGG G GG G GGGGGGGG GG GGGGG GG GG G GGGGGG GGG GGG GG G G GG G G GGGGGG GGGG GG GGGGG CC CC CCC C CCCCCCCCCCCCC C CCC C CC TT TTTTTT T TT TTTTTTTTTTTTTTTTTTTT TTT T TT TTTTTTTTTTTTTTTTTTTTT AAAAAA AAA AC CCCCCC C CCCCCCC C CCCCCCCCCC CCC C C CCCC C CCCCC C CC CCC C TTTTT TTTTTTT T TTTT T TTT T T T TTTTTTTTTTTTTT T TTTTTTTTTTT T TTTTTTTTTT TTTTTT T TTTTTT T TTTTT CCCCCCCCCCCCC C CCCCCC CCCCCCCCC CCC CCCCCCCCCCC CCCCCC C C T T TTTTTTTTT TTTTTTTTTTTTT T TTTTTTTTTTTT TTTT T TTTTTTTTT T T TT TTT TTT TTTTTTTTTTTTTT C CC CC CCCCCCCCC C C C CCC CCCCCCCC CCCCCCCCC C CCCCC CCCC AA A AAAAAAA AAAAA AA AAAA A AAAAAA A AAA AA A A A AAAAAA A A A AAAAAA A AA AAAA A A A A AAAA A AAAA 00 46526000 TT CCCCCCCCCCC CCCCCCCC C C C CCC CCCCCCCC CCCC AAAA AAAAAAA AAAAAAAAAA AAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAA AAAAAAAA A A TTTTTTTTT TTTTTTT TTTT T TTT TTT TTTT TTT T TTTT TTTTT TTTTT T T TTT T TTT T TTTTTTT T TT T T TTTTTTTTTTTTTTT T TT T TTTTTTT TTTT TTTTT G GGGG G GGGGG GGGG GGG G GGGGG GGGG G G GGGGG G T TTTTT TTTT T TTTT T T T TT TT T TTT TTTT T T T T T TTT TTTTT TT T T T T TT TT T T T T TT TTT C CC C CCCCCCCCCCCCCCCCCCCC CCCCCCCC AAAAAAAAAA AAA A G GGGGGGGGGGGGGGGGGGGGGGGG G G GGGGGGGGGG GGGGGGGGG GG GGGG GGG G GGGGGG GGGGG G GGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGGGG G GGGGGGGGGGGG GGGGGG G G CCCCCCCC C C CCCCCCCCCC CCCCCCC C CCCCCCCCC C CCCCCCCCCC CC C CCCCCCCCCCC C CCC CCCCCCCC CCCCCCC CC CCCCCCCCC CCC CCCCC C CCCC C CCCCCCCCCC CC CCCCC CT TT TTTTTTTTTTTTTTTTTTTTT D DD DDDDDDDD DDDDDDDDDDDDDDDDDDDDDDD DDD D DDDDDDDDDDDDDDDDDDDDDDA AAAAAA AAAAC CCCCCC C CCCCCCC C CCCCCCCCCC CCC C C CCCC C CCCCC C CC CCC C T T TT T T T T T T T T T TTT T T TT T T T T T T T T T T TT TT TT TT T TTTTT T T T T T T T TTT TT TTT TT T T T T T T T TTTTTT T T T T T T C C CC CCCCCC CCC C C CCCCC C CC CC C CCC CCC C CCCCC C CC CC CC CC CC C C T T TT TT TTT TT T T TTT T TTT T T TT T TT TT T T TTTTT T T TT T T T TT T TTT TT T T TT TTT TTT TTTTTTTTTT TTTT C CC CC CCCCCCCCC C C C CCC CCCCCCCC CCCCCC CCC C CCCCC CCCC AA A AAAAAAA AAAAAAA AAAA A AAAAAA A AAA AA A AAAAAAAA A A AAAAAAA A AA AAAA A A A AAAAAA AAAAAA G 00 46526000 TT CCCCCCCCCCC CCCCCCCC C C C CCC CCCCCCCC CCCC AAAA AAAAAAA AAAAAAAAA A AAAAAAAAAAAA AA AAAA AAAAA A AAAA AAA A AAAA AAA A A A TTTTTTTTT TTTTTTT TTTT TTTTTTTTTTT TTT T TTTTTTTTTTTTTTT T TTT T TTT T TTTTTTT T TTT T TTTTTTTTTTTTTTT T TTTTTTTTTTTTTT TTTTT G GGGG G GGGGG GGGG GGG G GGGGGGGGGG G GGGGG G T TTTTTTTTT TTTTT T T T TT TT T TTT TTTTT T T TTTTTTTTTTTTTT T TTT TT T TT T TTTTT C CC C CCCCCCCCCCCCCCCCCCCCCCCCCCCC AAAAAAAAAA AAA A G GGGGGGG GGGGGGGGGGGGG GGGG G G GGGGGGGGGG GGGG GGGGG GG GGGG GGG G GGGGGG GGGGG G GGGGGGG G GGG GGG G GGGG GGGGG GG GGGGGGG GGGGGGGGGGGGG GGG GGG G GGGGGG GGGGGG G GGGGG G G G GGGGGGG G G GGGG GGGGGG GGGGGGG G GGGGGGGG G G G G G GGGGGGG GG G GGG GGGGGGGG G GG G GGGGGGGG GG GGGGG GG GG G GGGGGG GGG GGG GG G G GG G G GGGGGG GGGG GG GGGGG CC CC CCC C CCCCCCCCCCCCC C CCC C CC TT TTTTTT T TT TTTTTTTTTTTTTTTTTTTT TTT T TT TTTTTTTTTTTTTTTTTTTTT AAAAAA AAA AC CCCCCC C CCCCCCC C CCCCCCCCCC CCC C C CCCC C CCCCC C CC CCC C TTTTT TTTTTTT T TTTT T TTT T T T TTTTTTTTTTTTTT T TTTTTTTTTTT T TTTTTTTTTT TTTTTT T TTTTTT T TTTTT CCCCCCCCCCCCC C CCCCCC CCCCCCCCC CCC CCCCCCCCCCC CCCCCC C C T T TTTTTTTTT TTTTTTTTTTTTT T TTTTTTTTTTTT TTTT T TTTTTTTTT T T TT TTT TTT TTTTTTTTTTTTTT C CC CC CCCCCCCCC C C C CCC CCCCCCCC CCCCCCCCC C CCCCC CCCC AA A AAAAAAA AAAAA AA AAAA A AAAAAA A AAA AA A A A AAAAAA A A A AAAAAA A AA AAAA A A A A AAAA A AAAA 00 46526000 1. Determine if multiple corrections “intersect” 2. Expand selection to entire region 3. Segment using mean changepoint
Toward a Basecaller Post correction and normalization distributions • Clearly some signal exists before complex machine learning • ~13% accuracy achievable by nearest mean calculations
Toward a Basecaller • Oxford Nanopore has recently upgraded to a RNN basecaller which produces reads with ~85% accuracy, thought it is still computationally intensive • Larger sequencer (PromethION) produces 12Tb of data in 48 hours (up to 1.44GBps) with current machine requiring ~1kW.
Toward a Basecaller Current event (base) segmentation is done using an FPGA t-test and all computation (RNN) is completed on the mean and SD of these segments We are currently working to integrate basecalling and segmentation directly from the raw data via an RNN with potentially vast improvements in accuracy as well as speed which will become increasingly important with throughput improvements. 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00 FPRate TPRate −2 −1 0 1 log10FDR
Challenges • Data Velocity • Basecaller must be able to keep up with the increasing speed of the data • Accuracy • Basecaller must be accurate enough to provide meaningful biological insight • Adaptabiltiy • Would like to be able to interrogate the data in order to assess confidence as well as possible alterations outside of the given model
Future Directions • Produce 1D basecalls on par with current algorithms ~70-80% • Exploring architectures and pre-processing • Investigate base alterations (methylation, acetylation, etc.) via encoding layers • Release package to create raw data training sets and provide QC metrics for raw reads.
Nanopore Sequencing Thanks!
References S https://en.wikipedia.org/wiki/Nanopore_sequencing S https://nanoporetech.com/how-it-works# S https://www.youtube.com/watch?v=qzusVw4Dp8w

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Nanopore sequencing .

Editor's Notes

  • #3 Single molecule Long read Publicly available through select community starting April 2014
  • #4 Single molecule Long read Publicly available through select community starting April 2014
  • #5 Single molecule Long read Publicly available through select community starting April 2014
  • #6 Single molecule Long read Publicly available through select community starting April 2014
  • #13 Single molecule Long read New chemistry (R7) showing as low as 26% error rate (for 2D reads) 37% error for 1D reads
  • #16 Single molecule Long read Publicly available through select community starting April 2014