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abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

arg-contig_mobilome_analysis

This pipeline performs a mobilome analyses on previously selected contigs

arg_ranker

argfams

Fast and robust identificaiton of antibiotic resistance genes (ARGs) from microbial genomes and metagenome assemblies using ARGfams, a high-quality and manually cruated subdatabase of profile hidden Markov models for ARGs

argminer

Curation of Antibiotic Resistance Genes by using crowdsourcing

args_oap

ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database

aviary

A hybrid assembly and MAG recovery pipeline (and more!)

basalt

biobakery

bioBakery tools for meta'omic profiling

biodata

All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")

bioinformatics-snakemake-pipelines

Collection of Snakemake pipeline for commin bioinformatics tasks

biosak

A Swiss-Army-Knife for Bioinformaticians

bioscripts-metauseful

some useful scripts for working with genomics and sequencing data

bit

Bioinformatics Tools

cariaco_basin

Scripts for analyses of particle-associated and free-living metagenomic and metatranscriptomic datasets from the permanently anoxic water column of the Cariaco Basin, Venezuela as part of the CARIACO Ocean Time Series project.

cat

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

coastal_sand_microbiota

R Codes for the analysis of 16S rDNA amplicon sequence data from the coastal sands

coelho2021_gmgcv1

compranking_taxonomy_tutorial

An tutorial for arg_ranker and tell the users how to gain the desired result step by step.

coverm

Read coverage calculator for metagenomics

cowtransfer-uploader

Simple Cowtransfer Uploader/Downloader in Golang

crassza

dada2

Accurate sample inference from amplicon data with single nucleotide resolution

decontam

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

deeptools

Tools to process and analyze deep sequencing data.

diting

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

dram

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

easymetagenome

Easy Metagenome Pipeline 2019 (1.0)

easymicroplot

R package for downstream Microbiome analysis

edge

EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.