Contamination Detection and Taxonomic confirmation with magicBLAST
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Check out what Rockstar Intern Sean La https://www.linkedin.com/in/sean-la-718b60103/?ppe=1 made after being at NCBI only 10 days (with a little help from our friends)!
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The document appears to be from a presentation given by Ben Busby on making the transition from sharing data to sharing knowledge. It discusses various tools and resources for accessing genomic data from the National Center for Biotechnology Information including EUtils, EDirect, PubMed FTP, and more. The presentation also highlights several genomic analysis tools and hackathon projects developed by the NCBI community.
Ncbi resources abrf_v3
This document summarizes Ben Busby's presentation on making the transition from sharing data to sharing knowledge at NCBI. The presentation discusses NCBI tools and resources like EUtils, EDirect, PubMed FTP, and SRA. It also highlights several genomic analysis tools developed through NCBI hackathons and available on GitHub. The document lists Busby's contact information and encourages attendees to check his SlideShare profile and NCBI's bioinformatics training program for more details.
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dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
The debris of the ‘last major merger’ is dynamically young
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Contamination Detection and Taxonomic confirmation with magicBLAST
- 1. Sean La Intern Simon Fraser University laseanl@sfu.ca Cheryl Ames, Ph.D. Research Fellow Smithsonian National Museum of Natural History amesc@si.edu Ben Busby, Ph.D. Genomics Outreach Coordinator NCBI ben.busby@nih.gov
- 2. 1. Image taken from https://media1.britannica.com/eb-media/82/126182-004-A23C1423.jpg 1 The scientific community wants to detect viruses in SRA SIDEARM SRR BLASTDB of Viruses Magic-BLAST (Optimized version of BLAST) BAM alignments to viruses Statistics Viral contigs Motivation 2 2. Image taken from https://github.com/NCBI-Hackathons/Virus_Detection_SRA
- 3. 1 1 Image taken from http://www.newhealthguide.org/images/19999893/image001.jpg 2 2 Image taken from https://3c1703fe8d.site.internapcdn.net/newman/gfx/news/hires/2014/auroraakinase.png Detect bacteria in metagenomics samples Identify proteins 3 Detect plasmid sequences in bacterial reads . 3 Image taken from https://upload.wikimedia.org/wikipedia/commons/thumb/c/cf/Plasmid_%28english%29.svg/300px-Plasmid_%28english%29.svg.png Detect mitochondrial DNA 4 4 Image taken http://www.penrules.com/_Media/art_mito_300.png
- 4. Step 6: Convert mitochondria-free files from SAM to FASTA format samtools fasta trimmed.read.nomtDNA.sam > trimmed.read.nomtDNA.fasta Step 5: Extract reads that don’t map to mtDNA database awk '$4 == 0 {print $0}' trimmed.read.sam >> trimmed.read.nomtDNA.sam Step 4: Create Magic-blast report (.sam) mapped & unmapped reads magicblast -query trimmed.read.fasta -db ala_mito_db -splice F -perc_identity 90 -paired > trimmed.read.sam & Step 3: Generate A. alata mtDNA database makeblastdb -in alatina_mitochondria.fasta -ala_mito_db -dbtype nucl Step 2: Trim adaptors from NGS data sets -- trimmomatic Illumina.fasta > trimmed.Illumina.fasta -- removesmartbell.sh Pacbio.fasta > trimmed.pacbio.fasta Step 1: Generate A. alata NGS data sets (n=15) Illumina.1.fasta=short reads (forward) Illumina.2.fasta=short reads (reverse) Pacbio.fasta =long reads A. alata 8 mitochondrial chromosomes (Genbank) Step 7: Pipe mitochondria-free reads (n=15) into downstream pipelines trimmed.reads.nomtDNA.fasta e.g., genome assembly box jellyfish A. alata
- 5. Neisseria meningitides genome (ERR1865236) BLAST DB of known bacterial plasmids SIDEARM 1 Image taken from https://upload.wikimedia.org/wikipedia/commons/thumb/c/cf/Plasmid_%28english%29.svg/300px-Plasmid_%28english%29.svg.png 1
- 6. Viral Metagenome (ERR1301508 a la Chris O’Sullivan) BLAST DB of complete bacterial genomes SIDEARM On SRA…. Using SIDEARM…
- 7. Greg Boratyn Mike Muchow Payl Cantalupo Alex Goncearenco Unix.systems 7
Editor's Notes
- Alatina alata has one of the most unusual mtDNA organizations in Metazoa, where genes are distributed on eight linear chromosomes with long terminal inverted repeats.