GENOME ASSEMBLY SNAPSHOT
FLOW-DIAGRAM
•Link the read files from /import/sequence/read-archive/
Link Files
•The goal here is to remove identical reads or reads-p...
Upcoming SlideShare
Loading in …5
×

Genome assembly snapshot flow diagram

256 views

Published on

0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
256
On SlideShare
0
From Embeds
0
Number of Embeds
33
Actions
Shares
0
Downloads
0
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Genome assembly snapshot flow diagram

  1. 1. GENOME ASSEMBLY SNAPSHOT FLOW-DIAGRAM
  2. 2. •Link the read files from /import/sequence/read-archive/ Link Files •The goal here is to remove identical reads or reads-pair. •It also helps in making the dataset size more manageableRedundancy Analysis •The goal here is to remove the adaptor sequences from the given data sets. •The adaptor are identified on the basis of information available from LIMS Adaptor Trimming •The goal is to remove all sequences which are below a certain threshold (15).Low Quality Score Filtering •The goal here is to remove all sequences that map to chloroplast and mitochondrial database based on their insert size.Contamination Analysis •The goal is to calculate the GC-content in the particular lane and plot a graph of the same.GC-content Analysis •The goal here is to understand the distribution of k-mer across the given dataset and thus estimating the genome size from the distribution.K-mer Analysis •The goal is to join the short overlap reads if present , to produce longer reads, therefore making it possible to span gaps or repeats in the genome.Join Reads •The goal here is to align and merge fragments of a longer DNA sequence to reconstruct the original sequence. •This is done using command line CLC Bio De novo assembler. Assembly

×