SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Pull mesh assignment from GEO using eutils, how ? tuku3 Bioinformatics 0 12-16-2013 11:48 PM
Taxonomic assignment discrepancies between SILVA and GenBank databases pmb0010 Metagenomics 1 05-12-2013 09:53 AM
contigs or reads for sequence search in a metagenomics run rathankar General 1 11-16-2012 05:16 AM
manual XS:A[-|+] assignment for cufflinks zorph Bioinformatics 4 05-07-2012 12:44 PM
Taxonomy classifier Chuckytah Bioinformatics 16 11-02-2011 12:55 PM

Reply
 
Thread Tools
Old 05-26-2014, 08:29 AM   #1
Gorbenzer
Member
 
Location: italy

Join Date: Apr 2012
Posts: 45
Default metagenomics contigs taxonomy assignment

Hi everyone,
i'm doing metagenomic assemblies of environmental samples rich in one species (>50% of the bacterial content is coming from a single species).

I got a good amount of contigs using Abyss (but if anyone have good suggestions i'll try other softwares) and i'll like to taxonomically assign my contigs in order to identify the contigs related to the high abundant species and analyze his gene content.

Can anyone suggest a good software for this purpose? I've found different tools for taxonomic assignment of single reads but not much for assembled contigs.

Thanks to anyone that will help
Gorbenzer is offline   Reply With Quote
Old 05-27-2014, 08:53 AM   #2
Gorbenzer
Member
 
Location: italy

Join Date: Apr 2012
Posts: 45
Default

up! anyone have suggestions?
Gorbenzer is offline   Reply With Quote
Old 05-28-2014, 01:11 PM   #3
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

blobplots? https://github.com/blaxterlab/blobology
maubp 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 08:14 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO