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a-microbiologist-wants-to-compute

This repo collects the list of learning online resources related to microbiome computational science and tools.

admixture-wrapper

A tool to automate analyses in admixture, a program used for detecting population structure with SNP data.

amrocks

Scripts used for Atlantis Massif crustal and sediment microbial analysis

ani

Calculate Average Nucleotide Identity (ANI) for prokaryotic genomes

aniclustermap

A tool for drawing ANI clustermap between all-vs-all microbial genomes using fastANI & seaborn

atlas

ATLAS - Three commands to start analyzing your metagenome data

automatic_mag_refinement

big-scape

Similarity networks of biosynthetic gene clusters

biokit

Bioinformatics in Python

biokit-1

a versatile toolkit for processing and analyzing diverse types of sequence data

camitax

CAMITAX: Taxon labels for microbial genomes

candidatus-nitrosopolaris

cat

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

cdna_cupcake

Miscellaneous collection of Python and R scripts for processing Iso-Seq data

challenger-deep-microbes

cold_adaptation

comebin

comparative_mycoplasma

Genome-resolved metagenomics suggests a mutualistic 2 relationship between Mycoplasma and salmonid hosts

contiguator

Bacterial genomes finishing tool for structural insights on draft genomes

coverage-based-functional-analyisis-in-a-mag-centric-view

A example of how to perform coverage-based functional analysis in a MAG-centric view across multiple samples

dada2_guidelines

A repository with a general dada2 pipeline for amplicon processing

diting

DiTing: A pipeline to infer and compare biogeochemical pathways in metagenomic data

dryad-app

Codebase for the collaboration of Dryad and Dash data publication and curation services.

ebame18

Long read metagenomics practical at EBAME18

ebame2022_quince_et_al

The tutorials developed by Chris Quince, Rob James and Sébastien Raguideau in EBAME7 2022

enrichm

Toolbox for comparative genomics of MAGs

falkormetat

Bioinformatic pipeline and data processing steps used to analyze eukaryotic metatranscriptomes

family_matters

All scripts used for generation of data in Family Matters manuscript

filtlong

quality filtering tool for long reads

firstchallenge_evaluation

Directory containing example result visualizations and scripts for generating figures and tables