Map reads to assembly

Usage

coverage(
  assembly_fn = "22030FL-06-02-140_assembly_1.fasta",
  paired_reads_1 = "extended_1_paired.fq",
  paired_reads_2 = "extended_2_paired.fq",
  unpaired_reads = "unpaired.fq",
  cpus = 4,
  outDir = NULL
)

Arguments

assembly_fn: Path to the input assembly file (fasta)
paired_reads_1: path to the raw forward input reads (fastq)
paired_reads_2: path to the raw reverse input reads (fastq)
unpaired_reads: path to the raw unpaired input reads (fastq)
cpus: Number of CPUs to use
outDir: Path to the output directory