minimap2: minimap2

In minimapR: Wrapper for 'minimap2'

minimap2

Description

This function is a wrapper for the command line tool minimap2. minimap2 is a long read sequencing alignment tool that is used to align long reads to a reference genome.

Usage

minimap2(
  reference,
  query_sequences,
  output_file_prefix = "minimap2_out",
  a = TRUE,
  preset_string = "map-hifi",
  threads = 1,
  return = FALSE,
  verbose = TRUE,
  ...
)

Arguments

reference	Reference genome to align the query sequences
query_sequences	Query sequences to align to the reference genome
output_file_prefix	Output file to save the alignment results
a	Logical value to use the preset string with the -a flag
preset_string	Preset string to use with the -x flag
threads	Number of threads to use
return	Logical value to return the alignment results
verbose	Logical value to print progress of the installation
...	Additional arguments to pass to minimap2

Value

This function returns the line needed to add minimap2 to PATH

Examples

## Not run: 
reference <- system.file("extdata/S288C_ref_genome.fasta.gz", package = "minimapR")
query_sequences <- system.file("extdata/yeast_sample_hifi.fastq.gz", package = "minimapR")
# Warning: not setting output_file_prefix will generate the output in the current working directory
bam_out <- minimap2(reference, 
 query_sequences, 
 threads = 4,
 preset_string = "map-hifi", 
 return = TRUE, 
 verbose = TRUE)

## End(Not run)

## Not run: 
reference <- system.file("extdata/GRCh38_chr1_130k.fa.gz", package = "minimapR")
query_sequences <- system.file("extdata/ont_hs_sample.fastq.gz", package = "minimapR")
# Warning: not setting output_file_prefix will generate the output in the current working directory
bam_out <- minimap2(reference, 
 query_sequences, 
 threads = 4,
 preset_string = "map-hifi",
 return = TRUE, 
 verbose = TRUE)

## End(Not run)

minimapR documentation built on April 12, 2025, 1:15 a.m.