Genomes

Supported reference genomes

These genomes are available on biowulf.

Reference Genomes

These genomes can be passed to the --genome parameter.

hg38

  • species: Homo sapiens
  • fasta: ${params.index_dir}/hg38_basic/hg38_basic.fa
  • genes_gtf: ${params.index_dir}/hg38_basic/genes.gtf
  • blacklist_index: ${params.index_dir}/hg38_basic/indexes/blacklist/hg38.blacklist_v3.chrM.chr_rDNA.*
  • reference_index: ${params.index_dir}/hg38_basic/bwa_index/hg38*
  • chromosomes_dir: ${params.index_dir}/hg38_basic/Chromsomes/
  • chrom_sizes: ${params.index_dir}/hg38_basic/indexes/hg38.fa.sizes
  • gene_info: ${params.index_dir}/hg38_basic/geneinfo.bed
  • effective_genome_size: 2700000000
  • meme_motifs: ${projectDir}/assets/HOCOMOCOv11_core_HUMAN_mono_meme_format.tar.gz
  • bioc_txdb: TxDb.Hsapiens.UCSC.hg38.knownGene
  • bioc_annot: org.Hs.eg.db

mm10

  • species: Mus musculus
  • fasta: ${params.index_dir}/mm10_basic/mm10_basic.fa
  • genes_gtf: ${params.index_dir}/mm10_basic/genes.gtf
  • blacklist_index: ${params.index_dir}/mm10_basic/indexes/blacklist/mm10.blacklist.chrM.chr_rDNA.*
  • reference_index: ${params.index_dir}/mm10_basic/indexes/reference/mm10*
  • chromosomes_dir: ${params.index_dir}/mm10_basic/Chromsomes/
  • chrom_sizes: ${params.index_dir}/mm10_basic/indexes/mm10.fa.sizes
  • gene_info: ${params.index_dir}/mm10_basic/geneinfo.bed
  • effective_genome_size: 2400000000
  • meme_motifs: ${projectDir}/assets/HOCOMOCOv11_core_MOUSE_mono_meme_format.tar.gz
  • bioc_txdb: TxDb.Mmusculus.UCSC.mm10.knownGene
  • bioc_annot: org.Mmu.eg.db

Spike-in Genomes

These genomes can be passed to the --spike_genome parameter.

dmelr6.32

  • species: Drosophila melanogaster
  • fasta: ${params.index_dir}/dmelr6.32/indexes/dmelr6.32.fa
  • reference_index: ${params.index_dir}/dmelr6.32/indexes/bwa/Drosophila_melanogaster.*
  • blacklist_index: ${params.index_dir}/dmelr6.32/indexes/blacklist/dmelr6.32.blacklist.*
  • blacklist_bed: ${params.index_dir}/dmelr6.32/indexes/dm6-blacklist.v2.no_chr.bed.gz

ecoli_k12

  • species: Escherichia coli K-12
  • fasta: ${params.index_dir}/ecoli_k12/indexes/ecoli_k12.fa
  • reference_index: ${params.index_dir}/ecoli_k12/indexes/ecoli_k12.*
  • blacklist_bed: NO_FILE

Custom reference genome

If you'd like to use a genome not available on Biowulf, you can prepare a custom genome with the MAKE_REFERENCE entrypoint. If you'd like to use a custom genome, you'll need the following files:

  • genome fasta
  • genome GTF
  • blacklist fasta

Prepare your custom reference genome with:

champagne run --output /data/$USER/champagne_project \
    --mode slurm -profile biowulf \
    -entry MAKE_REFERENCE \
    --outdir custom_genome \
    --genome custom_genome \
    --genome_fasta genome.fasta \
    --genes_gtf genome.gtf \
    --blacklist blacklist.fasta

The reference files and a config file for the genome will be written in results/genome/custom_genome/.

Then you can run champagne using your custom genome:

champagne run --output /data/$USER/champagne_project \
    --mode slurm -profile biowulf \
    --input samplesheet.csv \
    --genome custom_genome \
    -c results/genome/custom_genome/custom_genome.config