{"repo":"nf-core/eager","free":true,"listed":false,"github":"https://github.com/nf-core/eager","clone":"git clone https://github.com/nf-core/eager.git","description":"A fully reproducible and state-of-the-art ancient DNA analysis pipeline","language":"Nextflow","stars":214,"topics":["nextflow","ancientdna","adna","pipeline","pathogen-genomics","population-genetics","nf-core","workflow","metagenomics","bioinformatics"],"license":"MIT","category":"workflow-automation","readme_excerpt":"A fully reproducible and state-of-the-art ancient DNA analysis pipeline . [!IMPORTANT] nf-core/eager versions 2. are only compatible with Nextflow versions up to 22.10.6! Introduction nf-core/eager is a scalable and reproducible bioinformatics best-practise processing pipeline for genomic NGS sequencing data, with a focus on ancient DNA (aDNA) data. It is ideal for the (palaeo)genomic analysis of humans, animals, plants, microbes and even microbiomes. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible. The pipeline pre-processes raw data from FASTQ inputs, or preprocessed BAM inputs. It can align reads and performs extensive general NGS and aDNA specific quality-control on the results. It comes with docker, singularity or conda containers making installation trivial and results highly reproducible. Quick Start 1. Install nextflow ( =20.07.1 && Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment. 4. Start running your own analysis! 5. Once your run has completed successfully, clean up the intermediate files. See usage docs for all of the available options when runni","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/eager/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."}