Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
velvet columbus reference errors sfh838t De novo discovery 3 05-12-2014 04:54 AM
Unexpected results with HTseq-count drdna Bioinformatics 1 11-22-2012 09:41 AM
Columbus, Velvet color space SOLiD support pepperoni Bioinformatics 3 06-19-2012 04:18 AM
Unexpected FastQC results Rocketknight Illumina/Solexa 3 04-14-2012 02:37 AM
Reference sequence about Columbus for Velvet xxb0316 Bioinformatics 1 06-01-2011 05:10 AM

Thread Tools
Old 11-30-2018, 08:16 AM   #1
Junior Member
Location: IL

Join Date: Nov 2018
Posts: 1
Default Velvet Columbus unexpected results

Hi all,
I have recently tried using Velvet Columbus extension in order to preform reference guided assembly of a whole genome sequence.
I have tried using two references to which I mapped my read using BWA -
The better one had 99.57% of reads mapped (and a cover of 99.9% of the reference)
The worse one had only 84.54% of the reads mapped.

I tried assembling with velvet Columbus with both of the references (the rest of the parameters were the same).
Surprisingly, the worse reference had better result (225 contigs, L50 = 29) than the better reference (370 contigs, L50 = 39)

My question is, are those results plausible? I used velvet running on the BAM file produced by BWA with the same parameters exactly. Is there anything wrong that I could have done on the way?

Thank you a lot!!
Y.G is offline   Reply With Quote
Old 12-04-2018, 02:53 AM   #2
Location: Louisiana

Join Date: Nov 2013
Posts: 38

I wonder if the repetitive content of the two genomes had anything to do with the unexpected results with Velvet Columbus?
Gopo 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 12:47 PM.

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