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instrain

Bioinformatics program inStrain

irep

scripts for estimating bacteria replication rates based on population genome copy number variation

kegg-network-pipeline

kmcp

Accurate metagenomic profiling && Fast large-scale sequence/genome searching

kneaddata

Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

kodama

Fast hierarchical agglomerative clustering in Rust.

kraken2

The second version of the Kraken taxonomic sequence classification system

krakentools

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

krakenuniq

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

latex-mimosis

A minimal & modern LaTeX template for your (bachelor's | master's | doctoral) thesis

lightgbm

A fast, distributed, high performance gradient boosting (GBT, GBDT, GBRT, GBM or MART) framework based on decision tree algorithms, used for ranking, classification and many other machine learning tasks.

lindia

Extension package of linear regression diagonostic plots in ggplot2.

lookingglass

pretrained LookingGlass language model for biological read-length DNA sequences, and related models derived from transfer learning

lorikeet

Strain resolver for metagenomics

maaslin2

MaAsLin2: Microbiome Multivariate Association with Linear Models

maast

Microbial agile accurate SNP Typer

magphase

Phasing for metagenomics using PacBio long reads

magpurify2

Identify and remove contaminants from metagenome-assembled genomes

maldi-learn

Software library for Maldi-Tof preprocessing and machine learning analysis.

maldi_amr

Code for the paper "Antimicrobial resistance prediction in clinical isolates through machine learning on MALDI-TOF mass spectra"

maldi_pike

Code for 'Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra'

mash-dist-snakemake

megahit

Ultra-fast and memory-efficient (meta-)genome assembler

megaqc

Web application to collect and visualise data across multiple MultiQC runs.

metaanalysis_crc

Meta-analysis on human gut microbiota in Colorectal cancer

metabgc

A metagenomic strategy for harnessing the chemical repertoire of the human microbiome

metabgc-snakemake

metagraph

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

metamap

Snakemake workflow to map and quantify microbial genomes in metagenomic reads

metamdbg

MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.