Software
inStrain - Program for highly sensitive genome comparisons and microdiversity analysis
Author/contact: Matt Olm
Code - https://github.com/MrOlm/instrain
Paper - Olm et al, Nature Biotechnology 2021
dRep - De-replication of microbial genomes
Author/contact: 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
