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 1.0.2 Index]