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Software

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SCRuB

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(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

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A python implementation of mgpipe (Baldini et al., Bioinformatics 2019).

Meydan et al., JOSS 2023

We also contributed to:

CoPTR

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Efficient and accurate inference of microbial growth rates from metagenomic data.

SVFinder

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Detection of structural variants in microbial genomes using metagenomic data.

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