Go Back   SEQanswers > Applications Forums > Metagenomics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Help resolve a lab debate... lre1234 Bioinformatics 1 08-02-2015 10:56 PM
Code to bin reads that have been mapped thh32 Bioinformatics 8 02-27-2014 12:11 PM
analyze 16S metagenomic 200bp data to species level Gorbenzer Metagenomics 3 11-06-2012 07:06 AM
UCSC Bin indexing system desmo Bioinformatics 2 06-03-2012 11:49 PM
corona/bin/ begsch SOLiD 1 09-07-2009 07:55 AM

Thread Tools
Old 05-10-2016, 09:16 AM   #1
Junior Member
Location: Pittsburgh

Join Date: May 2016
Posts: 5
Default Resolve species/strain in metagenomic bin

Hi all,

I am trying to recover microbial draft genomes from metagenomic contigs.

I have used several assembly and binning tools to optimize my results (CLC, Spades, Vizbin, Maxbin, Metabat).
Since my samples were dominated by one genus the majority of the contigs belong to this taxa, resulting in one big bin, which based on the number of extracted 16S sequences contains multiple species or even strains of this genus. None of the binning tools I have worked with have been able to resolve the bin, leaving me with one big "pan-genome" bin that is very complete, but also very contaminated (according to checkm).

What is the best way to resolve the bin? Are other binning softwares that are more accurate? I know of tools that offer metagenomic strain resolution, however usually a database with multiple already sequenced genomes is necessary for those, which in my case is not really the case.

Thank you for any insights on this topic.

DL88 is offline   Reply With Quote
Old 06-01-2016, 04:53 AM   #2
Location: florida

Join Date: Jan 2013
Posts: 67

You can give LSA a try. The paper is here
yzzhang is offline   Reply With Quote
Old 06-03-2016, 10:27 AM   #3
Location: VA, USA

Join Date: Oct 2011
Posts: 18

Have you tried MyCC (
kopardev is offline   Reply With Quote

binning, draft genome, metagenomic

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 01:03 PM.

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