Hifiasm

Hifiasm

description
We run two HiFiasm jobs, one for getting alternative contigs and one for getting the haplotigs. And we take the primary assembly from the first job.

Inputs

Required

  • prefix (String, required): prefix to apply to assembly output filenames
  • reads (File, required): reads (in fasta or fastq format, compressed or uncompressed)

Optional

  • AssembleForAltContigs.runtime_attr_override (RuntimeAttr?)
  • AssembleForHaplotigs.runtime_attr_override (RuntimeAttr?)

Defaults

  • zones (String, default="us-central1-a us-central1-b us-central1-c us-central1-f")

Outputs

  • primary_gfa (File)
  • primary_tigs (File)
  • alternate_gfa (File)
  • alternate_tigs (File)
  • log_in_pVSa_mode (File)
  • phased_gfas (Array[File])
  • phased_tigs (Array[File])
  • log_in_hap_mode (File)
  • primary_gfa_in_hap_mode (File)
  • primary_tigs_in_hap_mode (File)

Dot Diagram

Hifiasm