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centrifuge

Classifier for metagenomic sequences

chat-gpt-google-extension

A browser extension to display ChatGPT response alongside Google Search results

conqur

Batch effects removal for microbiome data via conditional quantile regression

emergent-phases

fastspar

Rapid and scalable correlation estimation for compositional data

heritability

Heritability in plant breeding - R and SAS code examples

instrain

Bioinformatics program inStrain

maldiquant

Quantitative Analysis of Mass Spectrometry Data

maliampi

Maximum Likelihood Amplicon Pipeline

mashmap

A fast approximate aligner for long DNA sequences

metaphlan

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

micom

Python package to study microbial communities using metabolic modeling.

mmseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

motus

motus - a tool for marker gene-based OTU (mOTU) profiling

nanoclust

NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads

netcomi

Network construction, analysis, and comparison for microbial compositional data

netmoss

netmoss2

siamcat

R package for Statistical Inference of Associations between Microbial Communities And host phenoType

sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.

sparcc-2

spieceasi

Sparse InversE Covariance estimation for Ecological Association and Statistical Inference

vibrant

Virus Identification By iteRative ANnoTation

virsorter2

customizable pipeline to identify viral sequences from (meta)genomic data

woltka

Woltka: a versatile meta'omic data classifier