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archpi

Archaeology pieline for ancient genome and microbiome

awesome-microbiome-datasets

AMD: research power CPU

bap-bgiseq

Bacteria Genome Assembly Pipeline for BGISEQ Platform based on SnakeMake Pipeline Toolkit.

big-map

callpi

Calling SNP, SNV, CNV, and other genotyping information from metagenomics sequencing data

cami2-rhizosphere-assembly

Take the challenge

camipi

Upload data to CAMI community

camisim

CAMISIM: Simulating metagenomes and microbial communities

crisprpi

crosspi

Crosstalk of microbes, viruses and host

dbpi

A pipeline to construct a database catalogue for microbiome research

disktk

Fast disk, fast discovery

dnbtk

A toolkit to manage raw data from DNB sequencing platform

drepi

Dereplicate genomes or genes using fast way

flupi

Influenza viruses analysis pipeline

foldpi

Snakemake version of AlphaFold

galaxypi

genepi

A pipeline to construct a mini gene catalogue from metagenomics data

growpi

Microbial community grow rate profiling pipeline (WIP)

gtdb-rev

gtdb_kraken

Kraken(2) database based on the GTDB project

hifiasm-meta

hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.

hiprfish

instrain

Bioinformatics program inStrain

jobtk

Some utils related with Sun Grid Engine and SLURM system

journal-club

mash

Fast genome and metagenome distance estimation using MinHash

metapi

A general metagenomics data mining system focus on robust microbiome research

metapi-manuscript

Writting metapi manuscript using manubot and markdown since 2020

metapi-wrappers