Banfield Laboratory

University of California, Berkeley


inStrain - Program for highly sensitive genome comparisons and microdiversity analysis

Author/contact: Matt Olm

Code -

Paper - Olm et al, Nature Biotechnology 2021



dRep - De-replication of microbial genomes

Author/contact: Matt Olm

Code -

Paper - Olm et al, ISME 2017



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

Author/contact: Chris Brown

Code -

Paper - Brown et al, Nature Biotechnology 2016



EukRep - Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

Author/contact: Patrick West

Code -

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 -

Paper - Sieber et al, bioRxiv 2017



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

Author/contact: Chris Miller

Code -

Paper - Miller et al, Genome Biology 2011



Strainer - For analysis of population variation in community genomic datasets

Author/contact: John Eppley

Code -

Paper - Eppley et al, BMC Bioinformatics 2007