Aligns metagenomic shotgun reads against a reference.

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

align_short_reads(object, ...)

Arguments

object	An artifact or list of files.
...	Configuration arguments or a configuration object as obtained by config_align.

Value

A list with the generated alignments and some general diagnostics.

Examples

 NULL
#> NULL