Banfield Laboratory

University of California, Berkeley

Software

dRep - De-replication of microbial genomes

Author/conact: Matt Olm

Code - https://github.com/MrOlm/drep

Paper - Olm et al, ISME 2017

 

 

 

 

iRep - Estimating bacteria replication rates based on population genome copy number variation

Author/contact: Chris Brown

Code - https://github.com/christophertbrown/iRep

Paper - Brown et al, Nature Biotechnology 2016

 

 

 

 

EukRep - Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

Author/contact: Patrick West

Code - https://github.com/patrickwest/EukRep

Paper - West et al, bioRxiv 2017

 

 

 

 

DAS tool - Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy

Author/contact: Christian Sieber

Code - https://github.com/cmks/DAS_Tool

Paper - Sieber et al, bioRxiv 2017

 

 

 

 

EMIRGE - Reconstruction of full length ribosomal genes from short read sequencing data

Author/contact: Chris Miller

Code - https://github.com/csmiller/EMIRGE

Paper - Miller et al, Genome Biology 2011

 

 

 

 

Strainer - For analysis of population variation in community genomic datasets

Author/contact: John Eppley

Code - https://github.com/jmeppley/strainer

Paper - Eppley et al, BMC Bioinformatics 2007

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