{"repo":"nf-core/references","free":true,"listed":false,"github":"https://github.com/nf-core/references","clone":"git clone https://github.com/nf-core/references.git","description":"nf-core/references is a bioinformatics pipeline that build references, for multiple use cases","language":"Nextflow","stars":22,"topics":["genome","references","reproducibility","reproducible-research","reproducible-science","nextflow","nf-core","pipeline","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/references is a bioinformatics pipeline that build references, for multiple use cases. It is primarily designed to build references for common organisms and store it on AWS igenomes. From a fasta file, it will be able to build the following references: - Bowtie1 index - Bowtie2 index - BWA-MEM index - BWA-MEM2 index - DRAGMAP hashtable - Fasta dictionary (with GATK4) - Fasta fai (with SAMtools) - Fasta sizes (with SAMtools) - Fasta intervals bed (with GATK4) - MSIsensor-pro list With an additional annotation file describing the genes (either GFF3 or GTF), it will be able to build the following references: - GTF (from GFF3 with GFFREAD) - HISAT2 index - Kallisto index - RSEM index - Salmon index - Splice sites (with HISAT2) - STAR index - Transcript fasta (with RSEM) With a vcf file, it will tabix index it. Assets Assets are stored in references-assets. Credits nf-core/references was originally written by Maxime U Garcia Edmund Miller Phil Ewels. We thank the following people for their extensive assistance in the development of this pipeline: - Adam Talbot - Friederike Hanssen - Harshil Patel - Jonathan Manning Contributions and Support If you would like to contribute to this pipeline, please see the contributing guidelines. For further information or help, don't hesitate to get in touch on the Slack #references channel (you can join with this invite). How to hack on it 0. Have docker, and Nextflow installed 1. nextflow run main.nf Some thoughts on referen","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/references/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."}