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amplici

AmpliCI, a model-based algorithm for denoising Illumina amplicon data.

amplicon_analysis

amplimap

amplicon/smMIP mapping and analysis pipeline

amr

amr_finder

assay_validation

This is a web-app and workflow for computationally screening PCR-based assays

awesome-microbes

List of computational resources for analyzing microbial sequencing data.

awesome-nextflow

A curated list of nextflow based pipelines

calib

Calib clusters barcode tagged paired-end reads based on their barcode and sequence similarity.

callings-nf

GATK RNA-Seq Variant Calling in Nextflow

conterminator

Detection of incorrectly labeled sequences across kingdoms

dairydb

defq

Ultra-fast Multi-threaded FASTQ Demultiplexing

dram

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

eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

fastp

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

fastv

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

goalign

Goalign

graftm

GraftM - Rapid community profiles from metagenomes

insaflu

INSaFLU (“INSide the FLU”) is an influenza-oriented bioinformatics free web-based suite

jekesa

Jekesa (Illuminate) is an automated bash pipeline for bacterial whole genome assembly and typing using Illumina paired-end sequencing data.

kraken2

The second version of the Kraken taxonomic sequence classification system

metacurator

metaphlan

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

metapore

MetaPORE – Chiu Laboratory, University of California, San Francisco

metashot

MetaShot (Metagenomics Shotgun) is a complete pipeline designed for the taxonomic classification of the human microbiota members. In MetaShot, third party tools and new developed Python and Bash scripts are integrated to analyze paired-end (PE) Illumina sequences, offering an automated procedure covering all the analysis steps from raw data management to taxonomic profiling. It is designed to analyze both DNA-Seq and RNA-Seq data.

micropro

A microbial profiling framework for metagenomic analysis

muffin

hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

pacific

PACIFIC: A lightweight alignment-free deep-learning classifier of SARS-CoV-2 and co-infecting viral sequences

pokay

Report salient qPCR primer/probe or immune epitope mismatches info against a set of pathogen isolate genomes