SilasK

ipath3

Python wrapper for ipath3

16S-dada2

Snakemake pipeline for amplicon sequencing using dada2

statsplot

FastDrep

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Snakebread

Snakemake workflow for Metaphlan and Humann

2022-search-sra-with-mastiff

Tools and utilities for making use of mastiff

atlas

:earth_americas: ATLAS - a framework for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data.

Auto-GPT

An experimental open-source attempt to make GPT-4 fully autonomous.

CheckM2

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

genome-properties

genome_uploader

Python script to upload bins and MAGs to ENA (European Nucleotide Archive)

humann

HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

linguist

Language Savant. If your repository's language is being reported incorrectly, send us a pull request!

Metagenome-Profile

Metagenome-QC

Snakmake-workflow for qc

named_array

old_webpage_production

profiler

Fast profiler using mmseqs

quarto-report

Template for reports using Quarto.

quarto_article

silask.github.io

snake_plass

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

snakemake-wrapper-utils

Utility functions and classes shared between Snakemake wrappers

snakemake-wrappers

This is the development home of the Snakemake wrapper repository, see

StrainGE

strain-level analysis tools

Struo2

Scalable creating/updating of metagenome profiling databases

upload_genomes

use_subspecies_catalog

Use specific sourmash index to quantify bacterial taxa from metagenomic samples