ys4

hybracter

Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

gtdb-taxdump

GTDB taxonomy taxdump files with trackable TaxIds

sylph

ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.

skani

Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

mdmcleaner

MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs

2023-basecalling-benchmarks

itol.toolkit

Helper Functions for Interactive Tree Of Life (iTOL)

microbiomeExplorer

The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph N. Paulson.

glycowork

Package for processing and analyzing glycans and their role in biology.

pb-metagenomics-tools

Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics

panaroo

An updated pipeline for pangenome investigation

panstripe

post processing of bacterial pangenome gene presence/absence matrices

refseq_masher

Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database

Struo2

Scalable creating/updating of metagenome profiling databases

bacannot

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

Perfect-bacterial-genome-tutorial

charcoal

Remove contaminated contigs from genomes using k-mers and taxonomies.

pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

abritamr

A pipeline for running AMRfinderPlus and collating results into functional classes

Verticall

Recombination-free trees

genome-grist

map Illumina metagenomes to genomes!

bonito

A PyTorch Basecaller for Oxford Nanopore Reads

kingfisher-download

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

score-assemblies

Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)

CheckM2

Assessing the quality of metagenome-derived genome bins using machine learning

happi

A Hierarchical Approach to Pangenomics Inference

run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

hAMRonization

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

proteinfer

Deep networks for protein functional inference

dragonflye

:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads