Combine all BAM alignment files into a single one

Combine all BAM alignment files into a single one

Usage

do_combine_alignments(seq_tab, aln_dir, outdir, top_only = FALSE, cores = NULL)

Arguments

seq_tab

Sequence table as returned by do_infer_all_barcodes or downstream functions

aln_dir

Alignment directory (as provided to do_infer_all_barcodes)

top_only

include only the top taxon

cores

Number of cores to use (default: 1, unless getOption('DadaNanoBC.cores') is defined, or the DadaNanoBC_cores environment variable is set)

out_prefix

Output prefix for '.bam', '.bam.bai' and '.fasta' files

Value

Named list of output files