Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Calculation of pan- and core-genome Stegger Bioinformatics 9 04-09-2015 10:28 PM
How to call the core genome of bacteria NGS group Bioinformatics 6 08-06-2013 09:13 AM
Postdoc Computational Biology: ICGC whole pan-cancer genomes jankorbel Academic/Non-Profit Jobs 0 07-19-2013 10:49 PM
Calculate core and Pan genome of bacteria Mithril Bioinformatics 0 10-16-2012 07:51 AM
Bioinfo-core conference call on ChIP-Seq simonandrews Events / Conferences 5 10-05-2009 07:49 AM

Thread Tools
Old 01-16-2014, 11:09 AM   #1
Junior Member
Location: CA

Join Date: Jan 2011
Posts: 8
Default How to call SNPs for core genes from bacterial pan genomes

I have ~40 permanent draft bacterial genomes, and I've already obtained their core genes.

I know I could use MAUVE to align the genomes and find the SNPs; however, I don't have a powerful enough computer to do that.

So is there a way to do it in a less computational-heavy way? Command line programs are fine.

And, do I definitely need a reference genome when calling SNPs within these ~40 bacterial genomes? I mean, I have identified the variable nucleotides for the core genes, but I cannot say they are SNPs unless I compare them to a reference, right? However, it seems that when one uses MAUVE to align genomes and call SNPS, one does not have to include a reference genome in the alignment.

Thanks a lot for your help.

Last edited by ostrakon; 01-16-2014 at 11:15 AM.
ostrakon is offline   Reply With Quote
Old 01-17-2014, 12:59 AM   #2
Senior Member
Location: Budapest

Join Date: Mar 2010
Posts: 329

It depends on the 40 bacterial genomes. If those genomes come from the same strain, you do not need reference genome to find SNPs. In this case you can use dialign2, muscle or other multiple alignment programs.

If the genomes are different strains, you need reference genomes. In this case blast will help.
TiborNagy is offline   Reply With Quote
Old 01-17-2014, 10:19 AM   #3
Junior Member
Location: CA

Join Date: Jan 2011
Posts: 8

Thank you, TiborNagy. The ~40 bacterial genomes I have are from the same genus; however, I built their 16S tree, and found that some of them are not from the same species. So yes, I guess I need a reference genome for calling SNPs.

After my post here yesterday, I ran into a program called Wombac that aligns bacterial genomes with a reference genome based on bwa and samtools. As I tried it, it is pretty fast and less computational-heavy, and it outputs the VCF files and an alignment of SNPs. Hope this helps for anyone who would like to do the same thing.
ostrakon is offline   Reply With Quote

core genome; snp

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 01:40 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO