{"repo":"nf-core/viralrecon","free":true,"listed":false,"github":"https://github.com/nf-core/viralrecon","clone":"git clone https://github.com/nf-core/viralrecon.git","description":"Assembly and intrahost/low-frequency variant calling for viral samples","language":"Nextflow","stars":167,"topics":["viral","metagenomics","amplicon","assembly","variant-calling","illumina","pipeline","workflow","nextflow","nf-core"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intra-host/low-frequency variant calling for viral samples. The pipeline supports both Illumina and Nanopore sequencing data. For Illumina short-reads the pipeline is able to analyse metagenomics data typically obtained from shotgun sequencing (e.g. directly from clinical samples) and enrichment-based library preparation methods (e.g. amplicon-based: ARTIC SARS-CoV-2 enrichment protocol; or probe-capture-based). For Nanopore data the pipeline only supports amplicon-based analysis obtained from primer sets created and maintained by the ARTIC Network. 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 running the full-sized tests individually for each --platform option can be viewed on the nf-core website and the output directories will be named accordingly i.e. platform illumina/ and platform nanopore/ . The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 i","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/viralrecon/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."}