Aligns metagenomic shotgun sample against a reference

This method uses bowtie2 and should not be too sensitive to the used pre- processing.

align_bowtie2(reads, index_basename, threads = 1,
  alignment_folder = "alignments", bam = TRUE, bowtie2_path = NULL,
  samtools_path = NULL)

Arguments

reads

A data frame containing the paths to the forward and reverse reads in fastq format. Needs to have at least columns "id" and "forward". If the samples are paired you also need a column "reverse".
index_basename

Path and basename of the index against which to align.
threads

How many threads to use for bowtie2.
alignment_folder

A folder to which to save log output and the generated alignment.
bam

Whether to output alignments in BAM format (requires samtools).
bowtie2_path

Path to the bowtie executables.
samtools_path

Path to samtools.

Value

A data frame mapping the alignments to the sample IDs. It will contain the following columns:

  • idthe id of the sample

  • successwhether alignment executed without error

  • logthe log output for the alignment

  • alignmentthe file containing the alignment

Examples

 NULL
#> NULL