Information about the Reference Genomes

Following reference datasets are used for running analysis pipelines:

Human

Genome build hg38

• Fasta file: GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
• Gene set: Gencode (v36)

Human and mouse mixture

These mixed reference genomes are usually required for analysing only single cell samples.

Genome build hg19 and mm10 (from 10xgenomics)

• Transcriptome data: refdata-cellranger-hg19-and-mm10-2.1.0.tar.gz

List of resources

• Heng Li’s blog: Which human reference genome to use?
• Hg38 Fasta file for analysis pipeline
• About hg38 reference genome
• Gencode gtf

Change logs

• 29 January 2021
  • Moved to Gencode v36 build from v30
• 25th June 2019
  • Moved to Gencode v30 build from v28