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Software
SCRuB
(Source-tracking for Contamination Removal in microBiomes).
In silico removal of contamination from (microbial) counts data using process controls.
Austin et al., Nature Biotechnology 2023
pymgpipe
A python implementation of mgpipe (Baldini et al., Bioinformatics 2019).
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Meydan et al., JOSS 2023
CoPTR
Efficient and accurate inference of microbial growth rates from metagenomic data.
SVFinder
Detection of structural variants in microbial genomes using metagenomic data.
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