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Map merged reads to reference using minimap2 and process with samtools

Source: R/07_run_minimap2.R
run_minimap2.Rd

Map merged reads to reference using minimap2 and process with samtools

Usage

run_minimap2(
  merged_dir = "merged",
  reference,
  output_dir = file.path(merged_dir, "bam")
)

Arguments

merged_dir

Directory where merged fastq files are stored (default: "merged")

reference

Path to reference FASTA file

output_dir

Directory for BAM files (default: "merged/bam")

Value

Vector of commands run