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Software

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DEBIAS-M

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(Domain adaptation with phenotype Estimation and Batch Integration Across Studies of the Microbiome).

Interpretable inference and correction of processing bias across microbiome batches and studies.

Austin et al., bioRxiv 2024

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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

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pymgpipe

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

Meydan et al., JOSS 2023

SGVFinder2

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Detection of structural variants in microbial genomes using metagenomic data.

An updated and maintained version of SGVFinder (Zeevi et al., Nature 2019)

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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