Go Back   SEQanswers > General

Similar Threads
Thread Thread Starter Forum Replies Last Post
extra high coverage regions in exome sequencing data lyz1030 Bioinformatics 1 10-22-2012 02:26 AM
low 454 coverage combined with high solexa coverage strob Bioinformatics 7 10-07-2010 10:14 AM
Very high depth of coverage knott76 Bioinformatics 5 11-19-2009 12:27 AM

Thread Tools
Old 04-01-2015, 03:07 PM   #1
Location: Canada, Quebec

Join Date: Apr 2012
Posts: 53
Default too high sequencing coverage


I sequenced by Illumina MiSeq some phage genomes. Normally, with bacterial genomes, I have an average sequencing coverage of 75-90x. But with the phages (much more small genomes) the coverages are more than 1500x.

I have read at some places that a too high coverage might be "problematic". Is someone can explain to me why?

Should I perform a random subsampling of my reads to assemble at a lowest average coverage (~100x)?

Thank you,

Antony03 is offline   Reply With Quote
Old 04-01-2015, 03:17 PM   #2
Brian Bushnell
Super Moderator
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

It depends on what you want to do. Most assemblers have heuristics geared toward much lower coverage, on the order of 100 or less. Super-high coverage may give very fragmented assemblies; with low coverage a given error is typically unique, but with high enough coverage the same error may be seen multiple times, and actually assembled. That will create false branches on a DeBruijn graph that may be cut, causing fragmentation. Some assemblers may also simply not assemble very-high coverage areas for other reasons.

If you have fairly uniform coverage, subsampling is a good option. If you have variable coverage, normalization is a better choice.
Brian Bushnell is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 10:31 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO