Description

Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command.

Input

Name (Type)
Description
Pattern

fasta (file)

Reference genome FASTA file

*.{fasta,fa}

gtf (file)

Reference transcriptome GTF file

*.gtf

reference_name (string)

The name to give the new reference folder

str

Output

Name (Type)
Description
Pattern

reference (directory)

Folder containing all the reference indices needed by Cell Ranger

versions (file)

File containing software version

versions.yml
included in
scrnaseq
author
Github user ggabernet
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Tools

cellranger
10x Genomics EULA

Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.

support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov