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hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data

hifiasm-meta

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

honeybee-virome-2020

Pipeline for the analysis of Bonilla-Rosso et al. 2020. "Honey bees harbor a diverse gut virome engagin in nested strain-level interactions with the microbiota" PNAS.

ibs_virome

ieasemusic

网易云音乐第三方

jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

jmag_jvd

This is a repository of the codes used in the Tomofuji et al (prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features associated with diets, populations, and diseases).

kmcp

Accurate metagenomic profiling && Fast large-scale sequence/genome searching

kmersgwas

A library for running k-mers based GWAS

kover

Learn interpretable computational phenotyping models from k-merized genomic data

krakentools

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

lskscripts

A placeholder for all my random scripts. Some scripts might eventually graduate and go to their own projects, so don't be surprised if anything leaves in the future.

manuscripts

collection of scripts used in published manuscripts

metagem

A Snakemake pipeline for the generation of MAGs, reconstruction of GEMs, and simulation of cross-feeding interactions within microbial communities from lab cultures, human gut, ocean, plant-associated, and bulk soil microbiomes

metagenome

Metagenome analysis pipeline

metagenome_pipeline

Pipeline for automated quality control, processing and analysis of large datasets consistent of multiple metagenome samples.

metagenomic-benchmark

The code deposited in this site contains the necessary scripts to integrate, standardise and generate taxonomic annotation matrices at the eight basic levels of taxonomic lineage: domain, phylum, class, order, family, genus, species and subspecies. These tools provide the possibility of comparing taxonomic annotation results obtained by different methods and databases.

mgs-gut

Analysing Metagenomic Species (MGS)

microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.

microbiomestatplot

Interpretation and visualization of microbiome charts

myscripts

ngs-analysis

二代测序数据分析

ngs_learning

生物信息学交流资料

pathongs

Pathogen NGS Documentary

pb-metagenomics-tools

pb-metagenomics-tools

phenotypeseeker

Identify phenotype-specific k-mers and predict phenotype using sequenced bacterial strains

prgc

Comprehensive catalogs for microbial genes and metagenome-assembled genomes of the swine lower respiratory tract microbiome

prodigal

Prodigal Gene Prediction Software

program_scripts

python-100-days

Python - 100天从新手到大师