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Align Reads to Reference Genome

Source: R/alignment.R
bb_align.Rd

Wrapper for STAR, HISAT2, or minimap2 alignment tools. Checks that the selected aligner is available on the system PATH before running.

Usage

bb_align(
  fastq,
  genome_index,
  output_dir,
  aligner = c("STAR", "HISAT2", "minimap2"),
  threads = 4L,
  paired = FALSE,
  extra_args = NULL
)

Arguments

fastq

Character. Path(s) to FASTQ files. For paired-end, provide a character vector of length 2.

genome_index

Character. Path to genome index directory (STAR) or index prefix (HISAT2, minimap2).

output_dir

Character. Output directory for BAM files.

aligner

Character. One of "STAR", "HISAT2", "minimap2".

threads

Integer. Number of threads. Default 4.

paired

Logical. Paired-end mode. If TRUE, fastq must have 2 elements. Default FALSE.

extra_args

Character or NULL. Additional arguments to pass to the aligner.

Value

A list with components:

bam

Path to the output BAM file

stats

A data.frame with alignment statistics

command

The exact command that was executed

Examples

# \donttest{
# Requires STAR/HISAT2/minimap2 installed
# result <- bb_align("reads.fastq", "/path/to/index", "output/")
# }