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Draft diploid genome assembly

This pipeline performs reference-guided draft diploid genome assembly.

draft_assembly

Description

  • Partition long reads into haplotypes with WhatsHap.
  • Detect intervals with enough partitioned long-read coverage and extract their contained reads to perform assembly.
  • Trim the subreads with MECAT2.
  • Perform subinterval assembly with wtdbg2.
  • Polish contigs using subreads with Racon and Arrow.
  • Recalibrate the base quality of contigs and filter low-quality contigs.
  • Perform interval assembly with phasebook.
  • Detect structural errors in contigs with Sniffles2 and Jasmine.
  • Polish contigs using short reads with Freebayes.
  • Filter contig regions with switch errors by comparing assembly haplotype to SNV haplotype.
  • Mask the adaptor sequences in contigs.

Requirement

Configuration (draft_assembly.yaml)

The configuration file should contain:

samples: Specify the path to a text file listing all samples. The file must be space-delimited, with:

  • Column 1: Sample name
  • Column 2: Sample sex

sr_fastqs: Specify the paths to the paired-end short-read FASTQ files. Use {sample} as a wildcard; it will be automatically replaced with sample names from the samples file.

lr_hifi_fastqs: Specify the path(s) to PacBio HiFi long-read FASTQ files. Use {sample} as a wildcard.

lr_zmw_fastqs: Specify the path(s) to PacBio ZMW FASTQ files. Use {sample} as a wildcard.

lr_subreads_bam: Specify the path(s) to PacBio subreads BAM files. Use {sample} as a wildcard.

reference:

  • CHM13: Provide the path to the T2T CHM13 human reference genome (FASTA format, indexed by samtools faidx).

par_region: Path to the pseudoautosomal region (PAR) BED file for CHM13. This is used to correctly handle sex-chromosome reconstruction.

prefix: Prefix used for naming output files.

consensus_fasta (optional): Path to the sample-specific consensus FASTA file. If omitted, the workflow will use the default: c5_personal_ref/consensus_fasta/{sample}/{sample}.personal_ref.fasta

chain (optional): Path to the chain file describing coordinate mapping between CHM13 and the consensus assembly. If omitted, the workflow will use the default: c5_personal_ref/consensus_fasta/{sample}/{sample}.personal_ref.chain

sample_phased_vcf (optional): Path to the sample's phased VCF. If omitted, the workflow will use the default: c4_phase_snv/sample_vcf/{sample}/{sample}.shapeit.vcf.gz

Usage

snakemake -s Snakefile --cores 64 --jobs 64 --configfile config/draft_assembly.yaml --profile ./profile/config_local/

Output

The output file should contain:

  • c6_draft_assembly/sample_assembly/{sample}/assembly/{sample}.{hap1,hap2}.fasta: Draft diploid assembly of each sample