minimap2_align {FLAMES}R Documentation

Minimap2 Align to Genome

Description

Uses minimap2 to align sequences agains a reference databse. Uses options "-ax splice -t 12 -k14 –secondary=no fa_file fq_in"

Usage

minimap2_align(
  minimap2_prog_path = NULL,
  fa_file,
  fq_in,
  sam_out,
  no_flank = FALSE,
  bed12_junc = NULL
)

Arguments

minimap2_prog_path

Absolute path to the directory containing minimap2

fa_file

Path to the fasta file used as a reference database for alignment

fq_in

File path to the fastq file used as a query sequence file

sam_out

File path to the output SAM file

no_flank

Boolean; used if studying SIRV, to tell minimap2 to ignore additional bases

bed12_junc

file path to the gene annotations in BED12 format. If specified, minmap2 prefers splicing in annotations.

Value

file path to the given output BAM file, bam_out


[Package FLAMES version 0.99.31 Index]