Assembly and binning of metagenomes
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Updated
Jun 6, 2024 - Nextflow
Assembly and binning of metagenomes
Amplicon sequencing analysis workflow using DADA2 and QIIME2
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Assembly and intrahost/low-frequency variant calling for viral samples
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
(Meta-)genome screening for functional and natural product gene sequences
A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies
A simple nextflow pipeline for running kraken2 and bracken in a docker container
Pipeline for metagenome and metatranscriptome joint assembly
Assembly and intrahost / low-frequency variant calling for viral samples
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
screening metagenomes for arbitrary lineages, using gene-centric assembly methods and phylogenetics
A simple pipeline for bacterial assembly and quality control
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxa to identify (and remove) are Homo and Homo sapiens. Removal is optional.
Nextflow pipeline for the analysis of metagenomic short reads.
Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.
Parallelised and automated construction of metagenomic classifier databases of different tools
A bare-bones, ridiculously simple metagenomics pipeline for viruses using Kraken 2 written in Nextflow.
A pipeline for taxonomic classification and functional annotation of metagenomic reads. Based on MEDUSA
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