Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
SOAPdenovo kadiri.sreenu Introductions 3 09-06-2014 05:59 PM
Extending contigs N50 (SOAPdenovo)? condomitti Bioinformatics 9 01-17-2014 10:20 AM
Annotate contigs with BLAST hit names; remove contigs with no hit Bueller_007 Bioinformatics 10 02-27-2013 11:22 AM
Comparing Soapdenovo and Soapdenovo-Trans Kate.W Bioinformatics 0 08-06-2012 04:04 PM
SOAPdenovo for ABySS contigs narain Bioinformatics 3 04-16-2012 11:31 AM

Thread Tools
Old 05-15-2019, 05:30 AM   #1
Junior Member
Location: France

Join Date: May 2019
Posts: 3
Default SOAPdeNovo, get the contigs

Hello all,
I am writing this message because I will need help with SOAPDeNovo. Indeed, I made an assembly of Novo with this tool and I want to recover the final contigs. I'm outputting two files. The first file in .contig corresponding to contig sequences without using mate pair information . The second file is in .ScafSeq containing scaffold sequences.
On the SOAP website , it is specified that the final contigs can be extracted by decomposing the scaffold sequences at the level of the gap regions.
I would like to know how to achieve this decomposition in order to get the contigs?
Hoping that you could help me I wish you a great day.
(Sorry for my bad level in english)
obriht is offline   Reply With Quote
Old 05-21-2019, 06:55 AM   #2
Senior Member
Location: Germany

Join Date: Oct 2008
Posts: 415

Why not use the scaffolds ? These are the final contigs organised into scaffolds by using the supplied probably mate pair info. This is what I have always used.

If you still want the contigs, maybe just break the scaffolds at long N stretches ?

If its an illumina assembly, it is likely to be pretty awful. Long reads are the way to go these days as I'm sure you know.
colindaven is offline   Reply With Quote
Old 05-23-2019, 05:59 AM   #3
Junior Member
Location: France

Join Date: May 2019
Posts: 3

Hello, I want to thank you for your answer.
I wanted to recover contigs because I want to scaffolding from two files containing separate contigs.
Thank you very much for your response and your help
obriht 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 12:31 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO