SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
paired-end reads mapped to genome.. gene with only one direction of paired-end reads? danwiththeplan Bioinformatics 2 09-22-2011 02:06 AM
finding structural variations without paired reads mike.t Bioinformatics 3 05-05-2011 10:23 AM
PubMed: Structural variation in the chicken genome identified by paired-end next-gene Newsbot! Literature Watch 0 02-05-2011 02:11 AM
Insert size for paired end sequencing for identification of structural variation mimi_lupton Sample Prep / Library Generation 0 08-31-2010 06:29 AM
Structural Variation with 454 Reads wjeck 454 Pyrosequencing 2 11-20-2009 05:05 AM

Reply
 
Thread Tools
Old 01-07-2013, 04:09 AM   #1
RFo
Junior Member
 
Location: Switzerland

Join Date: May 2012
Posts: 5
Default Structural variation using paired-end reads

I have resequenced a bacterial genome using paired-end SOLiD reads (75+35 bp).

Which software is recommended to detect large insertions / deletions (and may be other structural variations) which makes use of the paired-end data?

I tried using LifeScope's LargeIndel detection tool, but apparently it's not very useful for prokaryotic genomes.

Along the same lines: which software would you use if you had Illumina data? Does Illumina have a standard software package to solve such a task?
RFo is offline   Reply With Quote
Reply

Tags
indel, paired end reads, structural variation

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 03:25 AM.


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