Running Verkko

Running Verkko#

Verkko supports multiple assembly configurations, depending on the available sequencing data and phasing resources. For comprehensive documentation, refer to the official Verkko repository: https://github.com/marbl/verkko.

Basic configuration: HiFi + ONT#

Use this configuration when both PacBio HiFi and ONT long reads are available.

verkko -d asm --hifi ./hifi.fastq.gz --nano ./ont.fastq.gz

If specific contaminant or auxiliary sequences are known in advance (for example, mitochondrial DNA or rDNA), include --screen to produce separate FASTA outputs and representative (exemplar) sequences.

verkko -d asm --hifi ./hifi.fastq.gz --nano ./ont.fastq.gz \
    --screen MT mt.fasta.gz \
    --screen rDNA rDNA.fasta.gz

Trio-informed assembly#

If sequencing data from both parents are available (commonly Illumina short reads), parental haplotype-specific k-mers can be used to improve phasing.

## Build parental hapmer databases (see Verkko documentation for details).

## Run Verkko with trio hapmer support.
verkko -d asm \
  --hifi hifi/*.fastq.gz \
  --nano ont/*.fastq.gz \
  --hap-kmers paternal_compress.k30.hapmer.meryl \
              maternal_compress.k30.hapmer.meryl \
              trio

Hi-C or Pore-C informed assembly#

Hi-C or Pore-C data can be incorporated to improve long-range phasing and scaffolding consistency.

verkko -d asm \
  --hifi hifi/*.fastq.gz \
  --nano ont/*.fastq.gz \
  --hic1 hic/*R1*fastq.gz \
  --hic2 hic/*R2*fastq.gz

Combined Hi-C and trio data#

This section will be provided in a future update.

# To be added

Using ONT-corrected reads#

Some workflows (for example, HiFiasm-based preprocessing) can generate ONT-corrected reads. Depending on the experimental design, these reads may be incorporated with HiFi data to increase effective backbone coverage.

# To be added
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