Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Reducing potentially chimeric contigs during assembly Rzinna De novo discovery 3 04-17-2014 10:22 AM
Finding contig repeat counts by mapping contigs to the reference genome misagh Bioinformatics 1 01-09-2014 05:41 AM
blast metagenome morning latte Bioinformatics 1 12-27-2013 06:10 PM
Metagenome assembly BIOin Metagenomics 10 09-26-2013 07:11 PM
Annotate contigs with BLAST hit names; remove contigs with no hit Bueller_007 Bioinformatics 10 02-27-2013 10:22 AM

Thread Tools
Old 10-16-2014, 01:54 PM   #1
Junior Member
Location: oxford, ohio

Join Date: Feb 2013
Posts: 3
Question Finding chimeric contigs in metagenome


I have contigs and read tracking file(.afg file) generated from Meta-velvet for a simulated metagenome. I am looking for chimeric contigs in the generated contigs. One idea which comes to my mind is to map the reads (from .afg file) to contigs and see if, two different read maps back to same contigs, assign that contig as chimeric.

Seeing the format of .afg file I am unable to decode it and hence proceed further. Anyone who has a prior experience working on this, please help. Also if you could suggest any other idea, It would be really helpful.

kumara is offline   Reply With Quote

bioinformatics analysis, metagenomes

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 07:36 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO