amplicon-pipeline 开源项目推荐（19 个）

EBI-Metagenomics /pipeline-v5

This repository contains all CWL descriptions of the MGnify pipeline version 5.0.

quadram-institute-bioscience /dadaist2

Dadaist2 🟨 Highway to R

yoann-dufresne /SLIM

A web app for environmental DNA metabarcoding analysis

Aveglia /vAMPirus

Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.

444thLiao /amplicon_workflow

amplicon analysisng pipelines based on luigi with qiime2-dada2/ qiime2-deblur/vsearch/usearch

sebrauschert /OceanOmics-amplicon

A pipeline to analyse marine fish amplicon data

Luke-B-Jones /NAP

Nanopore sequencing-based Amplicon Pipeline: optimised for full-length, 16S and 18S mixed amplicon datasets, in a fast and computationally efficient manner, setup for use of 515Y/926R primers, but also compatible with other cross-domain primers.

Nirmal2310 /NANOTAXI

An End-to-End GUI for real-time taxon identification via barcoded nanopore amplicon sequencing data. The pipeline is built using R Shiny library and majorly targets users with minimal coding background. Users can get from sequencing to results in a few clicks.

ozlemsagiroglu /auto16s

analyses paired-end 16S rRNA amplicon data, from raw FASTQ files to statistics and publication-ready figures

ohmeta /qiimepi

Snakemake version of QIIME2

jvtarss /ccm-2024

Aires-Teixeira, J. V., & Souza, E. (2025). Use of microbial fuel cell systems in wastewater treatment in connection with bioenergy generation. Desafios - Revista Interdisciplinar da Universidade Federal do Tocantins, 12(1), 1–20. https://doi.org/10.20873/pibic_2024_21014.

Mycology-Microbiology-Center /Minovar

Minovar pipeline

AldrichCPU-bio /microbes_scripts

scripts about microbial amplicon pipeline based on USEARCH

Marcus-Yaati /Bioinformatics_Fall_2025

The code from independent projects completed during bioinformatics in Fall 2025

mwslawinska /qiime2-snakemake-pipeline

QIIME2 + Snakemake pipeline for 16S rRNA amplicon analysis. Features: DADA2 denoising, taxonomic classification, and ASV count table generation. Conda (main) and Singularity/HPC (hpc branch) versions available.

AAFC-Bioinfo-AAC /microbiome-master-its

Microbiome-Master ITS is a user-friendly modular pipeline for processing raw ITS amplicons into ASVs using standard bioinformatic tools such as QIIME2, DADA2, etc. / Microbiome-Master ITS est un pipeline modulaire convivial pour le traitement d’amplicons ITS bruts en ASV à l’aide d’outils bioinformatiques standard tels que QIIME2, DADA2, etc.

ruben1294 /metabarcoding_ampliseq

Metabarcoding ampliseq: uso de nf-core/ampliseq para realizar metabarcoding. Adaptado para correr local o en HPC.

msuokas-bco /dada2_template

该项目在 GitHub 上没有填写描述

CCBR /CCBR_circRNA_AmpliconSeq

Snakemake workflow to process circRNA AmpliconSeq datasets generated to study circRNAs in KSHV and human hosts using divergent primers.