{"repo":"nf-core/taxprofiler","free":true,"listed":false,"github":"https://github.com/nf-core/taxprofiler","clone":"git clone https://github.com/nf-core/taxprofiler.git","description":"Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data","language":"Nextflow","stars":190,"topics":["metagenomics","profiling","taxonomic-profiling","shotgun","nf-core","nextflow","workflow","pipeline","classification","microbiome"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/taxprofiler is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data. It allows for in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, and produces standardised output tables for facilitating results comparison between different tools and databases. Pipeline summary 1. Read QC ( FastQC or falco as an alternative option) 2. Performs optional read pre-processing - Adapter clipping and merging (short-read: fastp, AdapterRemoval2; long-read: porechop, Porechop ABI) - Low complexity and quality filtering (short-read: bbduk, PRINSEQ++; long-read: Filtlong), Nanoq - Host-read removal (short-read: BowTie2; long-read: Minimap2) - Run merging 3. Supports statistics metagenome coverage estimation (Nonpareil) and for host-read removal (Samtools) 4. Performs taxonomic classification and/or profiling using one or more of: - Kraken2 - MetaPhlAn - MALT - DIAMOND - Centrifuge - Kaiju - mOTUs - KrakenUniq - KMCP - ganon - sylph - Melon - MetaCache 5. Perform optional post-processing with: - bracken 6. Standardises output tables ( Taxpasta ) 7. Present QC for raw reads ( MultiQC ) 8. Plotting Kraken2, Centrifuge, Kaiju and MALT results ( Krona ) 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 ","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/taxprofiler/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."}