Wednesday, October 29, 2014

Binning Metagenomic Contigs Using Coverage Profile Across Samples

This new category of binning methods - coverage(abundance)
pattern/vector/profile across different samples can be viewed as the
third - besides composition(k-mer spectrum)based and similarity-based
approach.


The first several papers related to this:

2012- Itai Sharon, Time series community genomics analysis reveals
rapid shifts in bacterial species, strains, and phage during infant
gut colonization
http://genome.cshlp.org/content/23/1/111

On time series samples.


2013 - Fredrik H. Karlsson Gut metagenome in European women with
normal, impaired and diabetic glucose control
http://www.nature.com/nature/journal/v498/n7452/full/nature12198.html

On multiple samples

2013- Mads Albertsen Genome sequences of rare, uncultured bacteria
obtained by differential coverage binning of multiple metagenomes
http://www.nature.com/nbt/journal/v31/n6/abs/nbt.2579.html

On two metagenomes generated from same sample

---
Above three papers didn't cite any other. Looks like they developed
the method separately.


2014 CONCOCT binning metagenomic contigs by coverage and composition
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3103.html

You must be aware of this paper. Sharon and Albertsen papers are cited.

2014 MetaHIT Consortium Identification and assembly of genomes and
genetic elements in complex metagenomic samples without using
reference genomes
http://www.nature.com/nbt/journal/v32/n8/abs/nbt.2939.html

Albertsen paper was cited.  

2014 GroopM: an automated tool for the recovery of population genomes
from related metagenomes
https://peerj.com/articles/603/

Newest paper on this - Published September 30, 2014

Seemingly these three 2014 papers were also developed separately.