SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Draft genome scaffolding with RNAseq paired-end reads JPZ Bioinformatics 7 02-10-2015 02:05 AM
scaffolding GAII paired-end library with Hiseq mate-pairs stevebaeyen Bioinformatics 17 02-27-2013 01:45 AM
scaffolding without paired-end, mate pair yifangt Bioinformatics 4 07-13-2012 08:52 AM
Tools to identify read pairs? Kennels Bioinformatics 1 04-30-2012 08:48 PM
Simulate Illumina read-pairs gene coder Bioinformatics 4 07-07-2011 03:37 AM

Reply
 
Thread Tools
Old 06-11-2015, 12:09 PM   #1
marct
Member
 
Location: Tempe, AZ

Join Date: Oct 2013
Posts: 11
Default re-scaffolding using BAC end read pairs

Hello,

I have a vertebrate genome assembly with contigs and scaffolds generated from ~80X PE Illumina small-insert and mate-pair libraries. There are also some BAC scaffolds and a few thousand BAC Sanger reads available for this species in the GenBank Trace database. I would like to use these publicly available data to merge scaffolds and improve on the Illumina-only assembly.

Aligning the assembled BAC scaffolds to the original genome scaffolds and generating consensus sequences to merge contigs/scaffolds seems fairly straightforward, can anyone recommend a method/pipeline that has worked for them? This was mentioned once here http://seqanswers.com/forums/showthr...ght=sspace+bac

I assume I can use the BAC end paired sequences with a scaffolding tool such as SSPACE (http://seqanswers.com/forums/showpos...6&postcount=11 ) but what is the best way to trim or at least incorporate quality scores? I don't think I want to simply use the raw traces downloaded from GenBank, unless anyone can convince me otherwise.


Thanks!
marct is offline   Reply With Quote
Reply

Tags
bac, bac scaffold, scaffolding, sspace

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 04:32 AM.


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