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fastp

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

free-programming-books

:books: Freely available programming books

freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

genome

the scripts of genome analysis

genomes-pipeline

MGnify genome analysis pipeline

gnomad-sv-pipeline

Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)

gut-metagenome-pipeline-based-on-nanopore-sequencing

hmp_client

Python-based client for downloading files hosted by the Human Microbiome Data Analysis and Coordination Center (hmpdacc.org).

hydra_single_cell

ideel

Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes

igv-snapshot-automator

Script to automatically create and run IGV snapshot batchscripts

instrain

Bioinformatics program inStrain

kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

krakenuniq

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

lathe

A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing

lathe-1

A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing

linux

Linux programming environment course in Chinese

long-read-assembler-comparison

Benchmarking of long-read assembly tools for bacterial whole genomes

maf2sam

Convert MIRA Assembly Format (MAF) to Sequence Alignment/Map (SAM) format

magcluster

Magnetosome gene cluster annotation, screening and visualization tool

magpy

Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)

mecat

MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

mecat2

metaboanalystr

R package for MetaboAnalyst

metagenome-sample-network-generator

A tool that generates a network of metagenomic samples positioned and with links according to the number of taxa shared

metagenomics_workflows

Workflows for metagenomic sequence data processing and analysis.

metamaps

Long-read metagenomic analysis

mgs-gut

Analysing Metagenomic Species (MGS)

micom

Python package to study microbial communities using metabolic modeling.

micop

MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.