Stars
Metagenomics-related extended functionalities to samtools
A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
More scalable dereplication for metagenome assembled genomes
Variational autoencoder for metagenomic binning
MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.
ARG normalization by mapping to the ARO ontology.
skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
GTDB taxonomy taxdump files with trackable TaxIds
ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs
Helper Functions for Interactive Tree Of Life (iTOL)
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 Jos…
Package for processing and analyzing glycans and their role in biology.
Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
An updated pipeline for pangenome investigation
post processing of bacterial pangenome gene presence/absence matrices
Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
Scalable creating/updating of metagenome profiling databases
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
Remove contaminated contigs from genomes using k-mers and taxonomies.
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!