Using reference genomes with refgenie
Reference genomes used in genomics pipelines can be accessed via refgenie.
Please refer to DANGPU user guide for more details.
In short, you can find available reference genomes like this:
module load python/3.8.16 refgenie/0.12.1a
refgenie list
which will output a list of available genomes.
Local refgenie assets
Server subscriptions: http://refgenomes.databio.org
┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ genome ┃ assets ┃
┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ GRCh38_ensembl │ fasta, ensembl_gtf, gencode_gtf, blacklist, star_index, bowtie2_index, bismark_bt2_index, 10x_index │
│ hg38_refgenie, hg38 │ fasta, gencode_gtf, ensembl_gtf, bwa_index, bowtie2_index, star_index, hisat2_index, │
│ │ cellranger_reference, bismark_bt2_index, fasta_txome, salmon_sa_index │
│ GRCm39_ensembl │ fasta, ensembl_gtf, bowtie2_index, star_index, bismark_bt2_index, 10x_index, blacklist │
│ dm6_ensembl │ fasta, bowtie2_index │
│ GRCh38_dm6 │ fasta, bowtie2_index │
│ GRCm39_dm6 │ fasta, bowtie2_index │
│ GRCh38_legacy │ fasta, gencode_gtf, blacklist, gtf_TE, star_index, bowtie2_index, bismark_bt2_index, 10x_index │
│ mm10_legacy │ fasta, gencode_gtf, blacklist, star_index, bowtie2_index, bismark_bt2_index, 10x_index │
│ dm6_FlyBase │ fasta, flybase_gtf, star_index, bowtie2_index, bismark_bt2_index │
│ puc19 │ fasta, bismark_bt2_index │
│ lambda │ fasta, bismark_bt2_index │
│ Spombe_h90 │ fasta, bowtie2_index │
│ Ecoli │ fasta, bowtie2_index │
│ sacCer3 │ fasta, ncbi_gff, star_index, bowtie2_index │
└─────────────────────┴───────────────────────────────────────────────────────────────────────────────────────────────────────────┘
You can further find contents of each reference genome using list -g option:
refgenie list -g GRCh38_ensembl
which gives you the information on available assets for the reference genome of interest:
Local refgenie assets
Server subscriptions: http://refgenomes.databio.org
┏━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━┓
┃ genome ┃ asset (seek_keys) ┃ tags ┃
┡━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━┩
│ GRCh38_ensembl │ fasta (fasta, fai, chrom_sizes, dir) │ release_111 │
│ GRCh38_ensembl │ ensembl_gtf (ensembl_gtf, ensembl_tss, ensembl_gene_body, dir) │ release_111 │
│ GRCh38_ensembl │ gencode_gtf (gencode_gtf, dir) │ release_45 │
│ GRCh38_ensembl │ blacklist (blacklist, dir) │ CUTANDRUN, ENCODE │
│ GRCh38_ensembl │ star_index (star_index, dir) │ 2.7.11b │
│ GRCh38_ensembl │ bowtie2_index (bowtie2_index, dir) │ 2.5.3 │
│ GRCh38_ensembl │ bismark_bt2_index (bismark_bt2_index, dir) │ 0.24.2 │
│ GRCh38_ensembl │ 10x_index (10x_index, dir, filtered_gtf) │ 7.2.0 │
└────────────────┴────────────────────────────────────────────────────────────────┴───────────────────┘
finally, you can find a path to a specific asset as <genome>/<asset>:<tag>
refgenie seek GRCh38_ensembl/blacklist:CUTANDRUN
which gives you a path to the asset file:
/maps/projects/dan1/data/RefGenomes_reNEW/alias/GRCh38_ensembl/blacklist/CUTANDRUN/GRCh38_ensembl_blacklist.bed.gz
Reference genome options for human (hg)
For human reference genome there are several options:
GRCh38_ensembl - the most updated reference genome that we suggest for new projects starting from 2024 and on. We currently use this as our default reference genome for human.
GRCh38_legacy - The human reference genome the Genomics Platform used 2017-2023.
GRCh38_dm6 - hybrid genome between GRCh38_ensembl and dm6_ensembl. This can be used for alignments when you have used spike-in from the fly. This reference contains only fasta and bowtie2 index.
GRCh38_refgenie (same as GRCh38) - the reference genome pulled from refgenie. Genomics Platform does not use this reference but it is available for users. Please note that if you run nf-core pipelines and use GRCh38 as reference genome, it will use GRCh38 from AWS_iGenomes reference genome instead of refgenie local list.
Reference genome options for mouse (mm)
For mouse reference genome there are also several options:
GRCm39_ensembl - the newest reference genome that we recommend for new projects starting from 2024 and on. This genome is the default reference genome for running Genomics Platform pipelines.
mm10_legacy - This is the mouse reference genome we used 2017-2023.
GRCm39_dm6 - hybrid genome between GRCm39_ensembl and dm6_ensembl. This can be used for alignments when you have used spike-in from the fly.
Other reference genomes
There are various spike-in genomes included in refgenie:
dm6_ensembl
dm6_FlyBase
puc19
lambda
Spombe_h90
Ecoli
sacCer3
Genomes in detail
Below you can find more detailed description of some of the main genomes.
GRCh38_ensembl
refgenie list -g GRCh38_ensembl
Local refgenie assets
Server subscriptions: http://refgenomes.databio.org
┏━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━┓
┃ genome ┃ asset (seek_keys) ┃ tags ┃
┡━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━┩
│ GRCh38_ensembl │ fasta (fasta, fai, chrom_sizes, dir) │ release_111 │
│ GRCh38_ensembl │ ensembl_gtf (ensembl_gtf, ensembl_tss, ensembl_gene_body, dir) │ release_111 │
│ GRCh38_ensembl │ gencode_gtf (gencode_gtf, dir) │ release_45 │
│ GRCh38_ensembl │ blacklist (blacklist, dir) │ CUTANDRUN, ENCODE │
│ GRCh38_ensembl │ star_index (star_index, dir) │ 2.7.11b │
│ GRCh38_ensembl │ bowtie2_index (bowtie2_index, dir) │ 2.5.3 │
│ GRCh38_ensembl │ bismark_bt2_index (bismark_bt2_index, dir) │ 0.24.2 │
│ GRCh38_ensembl │ 10x_index (10x_index, dir, filtered_gtf) │ 7.2.0 │
└────────────────┴────────────────────────────────────────────────────────────────┴───────────────────┘
Characteristics
This genome genome uses fasta (GRCh38.p14 primary assembly from soft-masked genome) and ensembl_gtf (Ensembl release 111) to generate star_index (using STAR 2.7.11b) bowtie2_index (using bowtie2 v.2.5.3) bismark_bt2_index (using bismark v.0.24.2) and 10x_index for GEX (using CellRanger v.7.2.0).
VERSION=111
wget -L http://ftp.ensembl.org/pub/release-${VERSION}/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz
wget -L http://ftp.ensembl.org/pub/release-${VERSION}/gtf/homo_sapiens/Homo_sapiens.GRCh38.${VERSION}.gtf.gz
Additional files
gencode_gtf: Gencode release 45
blacklist files contain regions prone to misalignment or bias in genomic analysis.
blacklist:ENCODE is sourced from ENCODE project for use with ATAC/ChIP-seq and
blacklist:CUTANDRUN is sourced from Nordin et al. 2023 for use with CUT&RUN.
Additional info
Chromosome names: 1, 2, 3, … , MT, X, Y Effective genome sizes can be found in deeptools documentation
GRCm39_ensembl
refgenie list -g GRCm39_ensembl
┏━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ genome ┃ asset (seek_keys) ┃ tags ┃
┡━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ GRCm39_ensembl │ fasta (fasta, fai, chrom_sizes, dir) │ release_111 │
│ GRCm39_ensembl │ ensembl_gtf (ensembl_gtf, ensembl_tss, ensembl_gene_body, dir) │ release_111 │
│ GRCm39_ensembl │ bowtie2_index (bowtie2_index, dir) │ 2.5.3 │
│ GRCm39_ensembl │ star_index (star_index, dir) │ 2.7.11b │
│ GRCm39_ensembl │ bismark_bt2_index (bismark_bt2_index, dir) │ 0.24.2 │
│ GRCm39_ensembl │ 10x_index (10x_index, dir, filtered_gtf) │ 7.2.0 │
│ GRCm39_ensembl │ blacklist (blacklist, dir) │ CUTANDRUN, EXCLUDERANGES │
└────────────────┴────────────────────────────────────────────────────────────────┴──────────────────────────┘
Characteristics
This genome references use fasta (GRCm39 primary assembly from soft-masked genome) and ensembl_gtf (Ensembl release 111) to build star_index for STAR v.2.7.11b, bowtie2_index for bowtie2 v.2.5.3, bismark_bt2_index for Bismark v.0.24.2. and 10x_index for Cellranger v.7.2.0.
VERSION=111
wget -L http://ftp.ensembl.org/pub/release-${VERSION}/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna_sm.primary_assembly.fa.gz
wget -L http://ftp.ensembl.org/pub/release-${VERSION}/gtf/mus_musculus/Mus_musculus.GRCm39.${VERSION}.gtf.gz
Additional files
blacklist files are included:
blacklist:EXCLUDERANGES from Ogata et al. 2023 for use with ChIPseq and ATACseq assays and
blacklist:CUTANDRUN from Nordin et al. 2023 for use with CUT&RUN and CUT&TAG assays.
Additional info
Chromosome names: 1, 2, 3, … , MT, X, Y
Effective genome sizes can be found in deeptools documentation
GRCh38_legacy
refgenie list -g GRCh38_legacy
Local refgenie assets
Server subscriptions: http://refgenomes.databio.org
┏━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━┓
┃ genome ┃ asset (seek_keys) ┃ tags ┃
┡━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━┩
│ GRCh38_legacy │ fasta (fasta, fai, chrom_sizes, hg38_chrom_sizes, dir) │ default │
│ GRCh38_legacy │ gencode_gtf (gencode_gtf, dir) │ default │
│ GRCh38_legacy │ blacklist (blacklist, dir) │ ENCODE │
│ GRCh38_legacy │ gtf_TE (gtf_TE, dir) │ default │
│ GRCh38_legacy │ star_index (star_index, dir) │ 2.7.2d │
│ GRCh38_legacy │ bowtie2_index (bowtie2_index, dir) │ default │
│ GRCh38_legacy │ bismark_bt2_index (bismark_bt2_index, dir) │ 0.22.3 │
│ GRCh38_legacy │ 10x_index (10x_index, dir) │ default │
└───────────────┴────────────────────────────────────────────────────────┴─────────┘
Characteristics
For GRCh38_legacy reference, fasta (Encode fasta GRCh38.p13) and gencode_gtf (from gencode.v32) were used to generate star_index using STAR v.2.7.2d, bowtie2_index using bowtie2 v2.3.4.1, bismark_bt2_index using bismark v0.22.3, gtf_TE for using with TETranscripts.
Additional files
10x_index: 10x index for GEX, issued by 10x in 2020 as refdata-gex-GRCh38-2020-A
blacklist: ENCODE blacklist sourced from nf-core/atac assets
Additional info
Chromosome naming: chr1, chr2, … chrM, chrX, chrY. Effective genome sizes can be found in deeptools documentation
mm10_legacy
┏━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━┓
┃ genome ┃ asset (seek_keys) ┃ tags ┃
┡━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━┩
│ mm10_legacy │ fasta (fasta, fai, chrom_sizes, dir) │ default │
│ mm10_legacy │ gencode_gtf (gencode_gtf, dir) │ default │
│ mm10_legacy │ blacklist (blacklist, dir) │ ENCODE, GUAVA │
│ mm10_legacy │ star_index (star_index, dir) │ 2.7.2d │
│ mm10_legacy │ bowtie2_index (bowtie2_index, dir) │ default │
│ mm10_legacy │ bismark_bt2_index (bismark_bt2_index, dir) │ 0.22.3 │
│ mm10_legacy │ 10x_index (10x_index, dir) │ GEX, GEX_GFP, ARC │
└─────────────┴────────────────────────────────────────────┴───────────────────┘
Characteristics
mm10_legacy genome references use fasta (GRCm38.p5 primary_assembly) and gencode_gtf (gencode vM15) to generate star_index for STAR v.2.7.2d , bowtie2_index and bismark_bt2_index for Bismark v.0.22.3.
Additional files
blacklist files are included:
blacklist:ENCODE from ENCODE and
blacklist:GUAVA from GUAVA
10x_index files (issued by 10x in 2020): 10_index:GEX for gene expression profiling, 10x_index:ARC for single cell ATAC. For internal use we have also generated , 10x_index:GEX_GFP for gene expression profiling with GFP reference included.
Additional info
Chromosome naming: chr1, chr2, … chrM, chrX, chrY.
Effective genome sizes can be found in deeptools documentation