Description

Module to build the reference needed by the 10x Genomics Space Ranger tool. Uses the spaceranger 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 Space Ranger

versions (file)

File containing software version

versions.yml
maintainer
Github user grst
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

spaceranger
10x Genomics EULA

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.

support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger