Reference Genomes

Updated: April 14, 2022
Edit this Page via GitHub Comment by Filing an Issue Have Questions? Ask them here.When analyzing data generated by high-throughput genome sequencing instruments, one common task is the comparison of those small genome fragments against a reference genome of a known organism. Because multiple groups may study the same organism, a collection of commonly used reference files have been made available for use in high-performance computing on the on-campus SLURM cluster.
iGenomes
The iGenomes collection of reference genomes
was developed by Illumina to provide a canonical source of reference genome information.
While that project is no longer actively updated, the available reference files have
been copied to a folder which is accessible at /shared/biodata/reference/iGenomes/
.
The structure of those files is described below, and moving forward additional
reference genome indices may be generated which follow the same format and structure.
File Structure
All files described below can be found within the directory /shared/biodata/reference/iGenomes/
:
-
The top-level folder in the iGenomes directory is named for the source organism: e.g.
/shared/biodata/reference/iGenomes/Homo_sapiens
; -
The second-level folder is named for the source of the annotation used for the reference genome: e.g.
/shared/biodata/reference/iGenomes/Homo_sapiens/UCSC
; -
The third-level folder is named for the version of the genome: e.g.
/shared/biodata/reference/iGenomes/Homo_sapiens/UCSC/hg19
; -
The fourth-level folders are
Annotation
andSequence
;-
The
Annotation
folder contains a folderGenes
and may also containSmallRNA
andVariation
. The exact files provided for each genome may vary, butGenes
may containgenes.bed
andgenes.gtf
to describe exon structure of genes, whileSmallRNA
may containhairpin.fa
andmature.fa
to describe miRNAs; -
The
Sequence
folder contains a folderWholeGenomeFasta
andChromosomes
which contain the FASTA sequence of the reference genome, either in full or broken out by chromosome, respectively; -
The
Sequence
folder also contains a set of references which have been pre-compiled for various alignment / analysis algorithms, which may include:BismarkIndex
BlastDB
Bowtie2Index
BowtieIndex
BWAIndex
MDSBowtieIndex
STARIndex
: For STAR < 2.7.6aSTAR2Index
: For STAR ≥ 2.7.6a
-
Example
Below is an example of the folders available for the UCSC human genome GRCh37/hg19 reference:
├── Homo_sapiens # Organism
│ └── UCSC # Source
│ ├── hg19 # Version
│ │ ├── Annotation
│ │ │ ├── Genes # Gene annotations
│ │ │ ├── README.txt
│ │ │ ├── SmallRNA # Small RNA annotations
│ │ │ └── Variation # Variant annotations
│ │ └── Sequence
│ │ ├── AbundantSequences
│ │ ├── BismarkIndex # Index for Bismark
│ │ ├── BlastDB # Index for BLAST
│ │ ├── Bowtie2Index # Index for Bowtie2
│ │ ├── BowtieIndex # Index for Bowtie
│ │ ├── BWAIndex # Index for BWA
│ │ ├── Chromosomes # Genome sequence by chromosome
│ │ ├── MDSBowtieIndex # Index for MDS Bowtie
│ │ ├── STARIndex # Index for STAR
│ │ ├── STAR2Index # Index for STAR2
│ │ └── WholeGenomeFasta # Genome sequence
RNA-Fusion Reference Database
In addition to the iGenomes references described above, the /shared/biodata/
volume also
hosts the reference files needed for the nf-core/rnafusion
analysis workflow.
The reference database was downloaded as described
with version 1.2.0
of nf-core/rnafusion
on January 18, 2022 to
/shared/biodata/reference/nfcore/rnafusion/1.2.0/2022-01-18
.
The content of that folder includes:
├── arriba/ # Reference database for the arriba tool
├── Homo_sapiens.GRCh38_r97.all.fa # Human reference genome sequence
├── Homo_sapiens.GRCh38_r97.cdna.all.fa.gz # Human reference transcript sequence
├── Homo_sapiens.GRCh38_r97.gtf # Human reference genome annotations
├── pipeline_info/ # Reference database download report
└── star-fusion/ # Reference database for the STAR-Fusion tool
Ongoing Support
To maintain the utility of this data resource, the Bioinformatics Core and the Data Core will incrementally add reference genomes for additional organisms and alignment algorithms. If your research group is interested in using an organism or alignment algorithm which is not currently available, please get in touch.
Updated: April 14, 2022
Edit this Page via GitHub Comment by Filing an Issue Have Questions? Ask them here.