Quast - NBISweden/workshop-genome_assembly GitHub Wiki

Quast: Reference sequence contiguity comparison

Notes:

  • -R ${REFERENCE} is not required, and only applicable if there is a reference to compare too.
  • --est-ref-size allows the calculation of NGx statistics such that they are comparable.

Command:

#!/usr/bin/env bash
module load bioinfo-tools quast
CPUS="${SLURM_NPROCS:-1}"

FASTA_DIR=/path/to/assemblies

EXPECTED_GENOME_SIZE=1000000
REFERENCE="/path/to/reference"

quast.py -R ${REFERENCE} --est-ref-size ${EXPECTED_GENOME_SIZE} $FASTA_DIR/*.fasta