demultiplex reads with flexiplex, for detailed description, see documentation for the original flexiplex: https://davidsongroup.github.io/flexiplex
Usage
flexiplex(
reads_in,
barcodes_file,
bc_as_readid,
max_bc_editdistance,
max_flank_editdistance,
pattern,
reads_out,
stats_out,
bc_out,
reverseCompliment,
n_threads
)Arguments
- reads_in
Input FASTQ or FASTA file
- barcodes_file
barcode allow-list file
- bc_as_readid
bool, whether to add the demultiplexed barcode to the read ID field
- max_bc_editdistance
max edit distance for barcode '
- max_flank_editdistance
max edit distance for the flanking sequences '
- pattern
StringVector defining the barcode structure, see [find_barcode]
- reads_out
output file for demultiplexed reads
- stats_out
output file for demultiplexed stats
- bc_out
WIP
- reverseCompliment
bool, whether to reverse complement the reads after demultiplexing
- n_threads
number of threads to be used during demultiplexing