{"repo":"nf-core/createtaxdb","free":true,"listed":false,"github":"https://github.com/nf-core/createtaxdb","clone":"git clone https://github.com/nf-core/createtaxdb.git","description":"Parallelised and automated construction of metagenomic classifier databases of different tools","language":"Nextflow","stars":22,"topics":["nextflow","nf-core","pipeline","workflow","database","database-builder","metagenomics","profiling","taxonomic-profiling","metagenomic-profiling"],"license":"MIT","category":"databases-storage","readme_excerpt":"Introduction nf-core/createtaxdb is a bioinformatics pipeline that constructs custom metagenomic classifier databases for multiple classifiers and profilers from the same input reference genome set in a highly automated and parallelised manner. It supports both nucleotide and protein based classifiers and profilers. The pipeline is designed to be a companion pipeline to nf-core/taxprofiler for taxonomic profiling of metagenomic data, but can be used for any context. 1. Prepares input FASTA files for building 2. Builds databases for: - Bracken - Centrifuge - Centrifuger - DIAMOND - ganon - Kaiju - KMCP - Kraken2 - KrakenUniq - MALT - sourmash - sylph - MetaCache Usage [!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data. First, prepare an input comma-separated table (csv) with your input reference genomes that looks as follows: id taxid fasta dna fasta aa ---------------------------------------- ------ ------------------------------------------- ------------------------------------------- Human Mitochondrial genome 9606 chrMT.fna SARS-CoV-2 genome 694009 GCA 011545545.1 ASM1154554v1 genomic.fna.gz GCA 011545545.1 ASM1154554v1 genomic.faa.gz Bacteroides fragilis genome 817 GCF 016889925.1 ASM1688992v1 genomic.fna.gz GCF 016889925.1 ASM1688992v1 genomic.faa.gz Candidatus portiera aleyrodidarum genome 91844 GCF 000292685.1 ASM29268v1 genomic.f","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/createtaxdb/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."}