{"repo":"nf-core/circdna","free":true,"listed":false,"github":"https://github.com/nf-core/circdna","clone":"git clone https://github.com/nf-core/circdna.git","description":"Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.","language":"Python","stars":35,"topics":["nf-core","nextflow","workflow","pipeline","circular","dna","ecdna","genomics","circle-seq","ampliconarchitect"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/circdna is a bioinformatics best-practice analysis pipeline for the identification of extrachromosomal circular DNAs (ecDNAs) in eukaryotic cells. The pipeline is able to process WGS, ATAC-seq data or Circle-Seq data generated from short-read sequencing technologies. Depending on the input data and selected analysis branch, nf-core/circdna is able to identify various types of ecDNAs. This includes the detection of smaller ecDNAs, often referred to as eccDNAs or microDNAs, as well as larger ecDNAs that exhibit amplification. These analyses are facilitated through the use of prominent software tools that are widely recognized in the field of ecDNA or circular DNA research. 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 on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/circdna/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."}