{"repo":"nf-core/mag","free":true,"listed":false,"github":"https://github.com/nf-core/mag","clone":"git clone https://github.com/nf-core/mag.git","description":"Assembly and binning of metagenomes","language":"Nextflow","stars":314,"topics":["workflow","nextflow","metagenomics","assembly","binning","annotation","nf-core","pipeline","bioinformatics","nanopore"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/mag is a bioinformatics best-practice analysis pipeline for assembly, binning and annotation of metagenomes. Pipeline summary By default, the pipeline currently performs the following: it supports both short and long reads, quality trims the reads and adapters with fastp, AdapterRemoval, or trimmomatic and Porechop, and performs basic QC with FastQC, and merges multiple sequencing runs. The pipeline then: - performs assembly using MEGAHIT and SPAdes, and checks their quality using Quast and ALE (if short read data is used) - (optionally) polishes long-read assemblies with short reads using pypolca - (optionally) performs ancient DNA assembly validation using PyDamage and contig consensus sequence recalling with Freebayes and BCFtools - predicts protein-coding genes for the assemblies using Prodigal, and bins with Prokka and optionally MetaEuk - performs metagenome binning using MetaBAT2, MaxBin2, CONCOCT, COMEBin, MetaBinner, and/or SemiBin2 - checks the quality of the genome bins using Busco, CheckM, or CheckM2 and optionally GUNC - Performs ancient DNA validation and repair with pyDamage and freebayes - optionally refines bins with DAS Tool - assigns taxonomy to bins using GTDB-Tk and/or CAT and optionally identifies viruses in assemblies using geNomad, or Eukaryotes with Tiara Furthermore, the pipeline creates various reports in the results directory specified, including a MultiQC report summarizing some of the findings and software versions. Usage [!N","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/mag/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}