{"repo":"nf-core/ampliseq","free":true,"listed":false,"github":"https://github.com/nf-core/ampliseq","clone":"git clone https://github.com/nf-core/ampliseq.git","description":"Amplicon sequencing analysis workflow using DADA2 and QIIME2","language":"Nextflow","stars":256,"topics":["amplicon-sequencing","16s","nf-core","nextflow","pipeline","workflow","metagenomics","rrna","18s","its"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nfcore/ampliseq is a bioinformatics analysis pipeline used for amplicon sequencing, supporting denoising of any amplicon and supports a variety of taxonomic databases for taxonomic assignment including 16S, ITS, CO1 and 18S. Phylogenetic placement is also possible. Multiple region analysis such as 5R is implemented. Supported is paired-end Illumina or single-end Illumina, PacBio and IonTorrent data. Default is the analysis of 16S rRNA gene amplicons sequenced paired-end with Illumina. A video about relevance, usage and output of the pipeline (version 2.1.0; 26th Oct. 2021) can also be found in YouTube and billibilli, the slides are deposited at figshare. On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website. Pipeline summary By default, the pipeline currently performs the following: - Sequencing quality control (FastQC) - Trimming of reads (Cutadapt) - Infer Amplicon Sequence Variants (ASVs) (DADA2) - Optional post-clustering with VSEARCH - Decontamination with decontam, if any controls or quantification information is given - Predict whether ASVs are ribosomal RNA sequences (Barrna","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/ampliseq/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."}