SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
New Resources for 1000 Genomes laura Bioinformatics 37 08-03-2020 05:22 PM
SPANNER (1000 genomes) Margarida Bioinformatics 11 12-04-2013 10:09 AM
1000 genomes - can anyone join in? henry.wood General 0 06-24-2011 05:21 AM
1000 Genomes Data RichardRocca General 1 03-16-2011 01:11 PM
1000 genomes Nataiki Bioinformatics 4 02-04-2011 05:42 AM

Reply
 
Thread Tools
Old 08-14-2014, 01:51 AM   #1
m4merg
Member
 
Location: Russia

Join Date: Jul 2014
Posts: 21
Default 1000 Genomes analysis workflow

Hello
I wonder was performed alignment on contigs in 1000 Genome project. I wanted to check frequency of huge insertions, but it is not possible to do if the alignment was done only on reference genome 37p13. I checked files on ftp server and didnt found anything that could help me. I've read documentation and as i understood right alignment was preformed only on reference. So I just want to get sure that i got everything right.

Thx in advance.
m4merg is offline   Reply With Quote
Old 08-15-2014, 05:49 AM   #2
m4merg
Member
 
Location: Russia

Join Date: Jul 2014
Posts: 21
Default

That's answer from their support if someone interested in:
Quote:
You are correct that the sequence reads were mapped to reference genome; the
project did not produce a de novo assembly from the reads.

The project did use several algorithms (cortex, SGA, and GATK haplotype caller)
that are based on reference free concepts for calling and validating variants;
however no de novo assembly was produced in the process.
m4merg is offline   Reply With Quote
Reply

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 03:45 PM.


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