{"repo":"nf-core/nanoseq","free":true,"listed":false,"github":"https://github.com/nf-core/nanoseq","clone":"git clone https://github.com/nf-core/nanoseq.git","description":"Nanopore demultiplexing, QC and alignment pipeline","language":"Nextflow","stars":228,"topics":["nf-core","nextflow","workflow","nanopore","demultiplexing","qc","alignment","pipeline"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nfcore/nanoseq is a bioinformatics analysis pipeline for Nanopore DNA/RNA sequencing data that can be used to perform basecalling, demultiplexing, QC, alignment, and downstream analysis. 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 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! On release, automated continuous integration tests run the pipeline on a full-sized dataset obtained from the Singapore Nanopore Expression Consortium 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 1. Demultiplexing ( qcat ; optional ) 2. Raw read cleaning (NanoLyse; optional ) 3. Raw read QC ( NanoPlot , FastQC ) 4. Alignment ( GraphMap2 or minimap2 ) - Both aligners are capable of performing ","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/nanoseq/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."}