{"repo":"nf-core/scrnaseq","free":true,"listed":false,"github":"https://github.com/nf-core/scrnaseq","clone":"git clone https://github.com/nf-core/scrnaseq.git","description":"Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection","language":"Nextflow","stars":349,"topics":["nf-core","nextflow","workflow","pipeline","10x-genomics","10xgenomics","alevin","bustools","cellranger","kallisto"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/scrnaseq is a bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data. This is a community effort in building a pipeline capable to support: - SimpleAF(Alevin-Fry) + qcatch - STARSolo - Kallisto + BUStools - Cellranger [!IMPORTANT] Cellranger is a commercial tool from 10X Genomics Inc. and falls under the EULA from 10X Genomics Inc. The container provided for the CellRanger functionality in this pipeline has been built by the nf-core community and is therefore not supported by 10X genomics directly. We are in discussions with 10X on how to improve the user experience and licence situation for both us as a community as well as 10X and end users and will update this statement here accordingly. Documentation The nf-core/scrnaseq pipeline comes with documentation about the pipeline usage, parameters and output. Usage [!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data. First, prepare a samplesheet with your input data that looks as follows: samplesheet.csv : Each row represents a fastq file (single-end) or a pair of fastq files (paired end). Now, you can run the pipeline using: [!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration e","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/scrnaseq/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."}