Generates multiplexing designs for amplicon-sequencing diversity analysis using tagged primers
python setMultiplex.py [-h] -i [I] -o [O] -f [F [F ...]] -r [R [R ...]] -n [N] [-l L L] [-m [M]] [-s [S]] [-rm [RM [RM ...]]] [-rmCombi [RMCOMBI [RMCOMBI ...]]] [-set [SET [SET ...]]] [--one] [--nolog] [--random] [--brute] [--verbose]
-h, --help Show help message and exit
-i [FILE] Tagged primers fasta file
-o [FILE] Output file name
-f [F [F ...]] Forward primer generic name
-r [R [R ...]] Reverse generic name
-n [N] Number of combinations to design. Enter different
numbers in the same order of the different tags files
-l L L Lengths of the forward and reverse tags
(default = [8, 8])
-m [M] Set a maximum primer usage frequency (automatically
changed if too low to be possible) (default = 0)
-s [S] Step-spacing between subsequent primers (if case of
sequencial cross-contamination of the primers and if
alphanumeric primer names) (default = 3)
-rm [RM [RM ...]] Single tagged primers not to include (either provide
file(s) with single primer name(s) in line(s), or
write it fully as space-separated arguents e.g. "V4F-4
F1-A")
-rmCombi [RMCOMBI [RMCOMBI ...]]
File(s) with the combinations to avoid (fully written,
space separated)
-set [SET [SET ...]] Restict the choice of multiplexing design(s) to a list
of combinations (file(s) with forward and reverse
primers names in 1st and 2nd columns, respectively
--one Get the first selection only (default: off)
--nolog Write a log file with the tested combination sets
(default: on)
--random Make random selection of mulitplexing design (default:
off)
--brute Make selection using brute-force algorithm based on
forward primers selection first and then reverse
primers until criteria satisfied (default: off)
--verbose Print ongoing processes and results to stdout
(default: off)
Python2.7
Biopython