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Search results for pipeline metagenomics

40 search results found

Squeezemeta ⭐ 308

A complete pipeline for metagenomic analysis

Assembly and binning of metagenomes

Sunbeam ⭐ 157

A robust, extensible metagenomics pipeline

Ampliseq ⭐ 141

Amplicon sequencing analysis workflow using DADA2 and QIIME2

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

Viralrecon ⭐ 101

Assembly and intrahost/low-frequency variant calling for viral samples

Taxprofiler ⭐ 78

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

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

Funcscan ⭐ 49

(Meta-)genome screening for functional and natural product gene sequences

Microbiomebestpracticereview ⭐ 45

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

Scalable creating/updating of metagenome profiling databases

Ley Lab MetaGenome Profiler DataBase generator

Covid 19 Signal ⭐ 32

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

Wochenende ⭐ 30

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3

Geneshot ⭐ 25

Pipelines ⭐ 20

Pipeline V5 ⭐ 19

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

Ebi Metagenomics Cwl ⭐ 19

This repository contains the CWL description of the EBI Metagenomics pipeline

Metameta ⭐ 18

Metasub_cap ⭐ 16

A comprehensive pipeline for short read metagenomic data

Tools and utilities for running Dockerized metagenomics tools in the Cloud

Tracespipe ⭐ 16

Reconstruction and analysis of viral and host genomes at multi-organ level

Virus metagenomic pipeline for unknown host or in absence of a host genome

Microbiome_notes ⭐ 13

A continually expanding collection of microbiome analysis tools

Flexible omics pipeline

Snakemake workflow for comparison of differential abundance ranks

AMR/VF LGT focused bacterial genomics analysis workflow

MineYourSymbiont : Targetted genome assembly for metagenomics pipeline.

Hackathon_v001_metagenomics ⭐ 11

Metagenomics Pipeline Repository for January, 2015 NCBI/ADDS Hackathon at NIH

Nxf Kraken2 ⭐ 10

A simple nextflow pipeline for running kraken2 and bracken in a docker container

Assembly and intrahost / low-frequency variant calling for viral samples

Blast Filtering Pipeline ⭐ 10

A very simple BLAST filtering pipeline

Snakemake based framework for NGS data analysis and management

Shotgun Metagenomics Pipeline ⭐ 8

A pipeline for primary analysis of shotgun metagenomic sequencing data

Metassemble ⭐ 7

Scripts to run several metagenomics assembly programs

zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics

Findfungi ⭐ 7

A pipeline for the identification of fungi in public metagenomics datasets

Tofu Maapo ⭐ 6

Nextflow pipeline for the analysis of metagenomic short reads.

Mikrokondo ⭐ 6

A simple pipeline for bacterial assembly and quality control

Sars Cov2_analysis ⭐ 5

Documentation for analyzing SARS-Cov2 samples.

Metasequencing ⭐ 5

A metagenomics pipeline using the CGAT framework.

Bioinformatics_pipeline ⭐ 5

Bioinformatics Pipeline

Metagenomics ⭐ 5

Snakemake workflow for functional analysis of metagenomic WGS read data.

Pipeline to pull microbial reads from WGS data and perform metagenomic analysis

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