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The Top 23 Pipeline Metagenomics Open Source Projects

Open source projects categorized as Pipeline Metagenomics
Categories > Metagenomics
Categories > Data Processing > Pipeline
Squeezemeta ⭐ 308
A complete pipeline for metagenomic analysis
total releases 2most recent commit 4 months ago
Mag ⭐ 164
Assembly and binning of metagenomes
most recent commit 4 months ago
Sunbeam ⭐ 157
A robust, extensible metagenomics pipeline
most recent commit 3 months ago
Ampliseq ⭐ 141
Amplicon sequencing analysis workflow using DADA2 and QIIME2
most recent commit 4 months ago
Eager ⭐ 112
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
most recent commit 4 months ago
Viralrecon ⭐ 101
Assembly and intrahost/low-frequency variant calling for viral samples
most recent commit 7 months ago
Taxprofiler ⭐ 78
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
most recent commit 3 months ago
Aviary ⭐ 62
A hybrid assembly and MAG recovery pipeline (and more!)
total releases 19most recent commit 4 months ago
Funcscan ⭐ 49
(Meta-)genome screening for functional and natural product gene sequences
most recent commit 3 months ago
Microbiomebestpracticereview ⭐ 45
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
most recent commit 2 years ago
Struo2 ⭐ 42
Scalable creating/updating of metagenome profiling databases
most recent commit a year ago
Struo ⭐ 40
Ley Lab MetaGenome Profiler DataBase generator
most recent commit a year ago
Covid 19 Signal ⭐ 32
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
most recent commit a year ago
Wochenende ⭐ 30
Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
most recent commit 2 years ago
Geneshot ⭐ 25
most recent commit 2 years ago
Pipelines ⭐ 20
RPD Pipelines
most recent commit 5 years ago
Pipeline V5 ⭐ 19
This repository contains all CWL descriptions of the MGnify pipeline version 5.0.
most recent commit 9 months ago
Ebi Metagenomics Cwl ⭐ 19
This repository contains the CWL description of the EBI Metagenomics pipeline
most recent commit 3 years ago
Metameta ⭐ 18
most recent commit 5 years ago
Metasub_cap ⭐ 16
A comprehensive pipeline for short read metagenomic data
most recent commit 4 years ago
Chiron ⭐ 16
Tools and utilities for running Dockerized metagenomics tools in the Cloud
most recent commit 5 years ago
Tracespipe ⭐ 16
Reconstruction and analysis of viral and host genomes at multi-organ level
most recent commit 10 months ago
Metavic ⭐ 15
Virus metagenomic pipeline for unknown host or in absence of a host genome
most recent commit 5 years ago
The 4 Latest Releases In Pipeline Metagenomics Open Source Projects
Aviary ⭐ 62
A hybrid assembly and MAG recovery pipeline (and more!)
total releases 19latest release November 20, 2023most recent commit 4 months ago
Squeezemeta ⭐ 308
A complete pipeline for metagenomic analysis
total releases 2latest release September 18, 2023most recent commit 4 months ago
Ymp ⭐ 13
Flexible omics pipeline
total releases 6latest release August 17, 2020most recent commit 3 years ago
Assnake ⭐ 10
Snakemake based framework for NGS data analysis and management
total releases 9latest release March 26, 2020most recent commit 3 years ago
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