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

hg19¶

• species: Homo sapiens
• fasta: ${params.index_dir}/hg19_basic/hg19.fa
• genes_gtf: ${params.index_dir}/hg19_basic/genes.gtf
• blacklist_index: ${params.index_dir}/hg19_basic/indexes/blacklist/hg19.blacklist.*
• reference_index: ${params.index_dir}/hg19_basic/bwa_index/hg19.*
• chromosomes_dir: ${params.index_dir}/hg19_basic/Chromosomes
• chrom_sizes: ${params.index_dir}/hg19_basic/Chromosomes/chrom.sizes
• gene_info: ${params.index_dir}/hg19_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

hs1_chrR¶

• species: Homo sapiens
• description: Human T2T-CHM13v2.0 with ribosomal DNA
• fasta: ${params.index_dir}/hs1_chrR/hs1_chrR.fa
• genes_gtf: ${params.index_dir}/hs1_chrR/hs1_chrR.genes.gtf.gz
• blacklist_index: ${params.index_dir}/hs1_chrR/blacklist/*
• reference_index: ${params.index_dir}/hs1_chrR/reference/*
• chromosomes_dir: ${params.index_dir}/hs1_chrR/chroms/
• chrom_sizes: ${params.index_dir}/hs1_chrR/hs1_chrR.chrom.sizes
• gene_info: ${params.index_dir}/hs1_chrR/hs1_chrR.genes.bed
• effective_genome_size: 2723047107
• meme_motifs: null
• bioc_txdb: null
• bioc_annot: null

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
• effective_genome_size: 142573017
• chrom_sizes: ${params.index_dir}/dmelr6.32/chrom_dmelr6.28.sizes

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
• effective_genome_size: 4641652
• chrom_sizes: ${params.index_dir}/ecoli_k12/Chromosomes/chrom.sizes

Custom blacklist¶

If you'd like to override the default blacklist used by one of the built-in genomes, you can provide a custom blacklist bed file or fasta file:

champagne run --output /data/$USER/champagne_project \
    --mode slurm \
    --genome hg38 \
    --blacklist /path/to/blacklist.bed

If you're providing a custom blacklist bed file, make sure its regions refer to the genome version you're using.

Custom reference genome¶

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

• genome fasta
• genome GTF
• blacklist fasta or bed (optional)

Prepare your custom reference genome with:

champagne run --output /data/$USER/champagne_project \
    --mode slurm \
    --build_reference \
    --genome custom_genome \
    --genome_fasta genome.fasta \
    --genes_gtf genome.gtf \
    --blacklist blacklist.bed

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

Alternatively, you can build the reference genome and run the rest of the pipeline in one shot by specifying the custom files like so:

champagne run --output /data/$USER/champagne_project \
    --mode slurm \
    --genome custom_genome \
    --genome_fasta genome.fasta \
    --genes_gtf genome.gtf \
    --blacklist blacklist.bed