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atlas

ATLAS - Three commands to start analysing your metagenome data

bigsi_rs

Rust in-memory implementation of a BIGSI-like data structure

checkm

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

clonalframeml

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

colorid

Experiments with using BIGSI data structure for metagenomic and QC applications

cortex

reference free variant assembly

fani2tree

A R script to create an ANI-based UPGMA tree from fastANI output

fastbloom

A fast bloom filter implemented by Rust for Python! 10x faster than pybloom!

gtdb_kraken

Kraken(2) database based on the GTDB project

mcoutbryk

SNP calling pipeline using mccortex

mockcommunity

Long-read mock community experiments

n50.sh

bash script to quickly produce some assembly stats

phylo_misbehave

pysnpsites

Experiments optimising python (with Cython)

retailbiofilmstudy

Rscripts and data for analyses of microbiota found in drains in retail delis

salmid

Rapid confirmation of Salmonella spp. and subspp. from sequence data

scoary

Pan-genome wide association studies

sepia

taxonomic classifier based on the kraken2 algorithms and more

seqsero

Salmonella serotyping from genome sequencing data

seqsero2

SeqSero2 alpha test

seqserok

A k-mer based implementation of SeqSero

sra_seqseroandispcr

pipeline for download, assembly and in silico PCR for primer testing in python

succession_fecal_microbiomes

treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

treetoreads

Pipeline to generate NGS reads from a phylogeny