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MASKPRIMERS.PY(1) User Commands MASKPRIMERS.PY(1)

NAME

MaskPrimers.py - Removes primers and annotates sequences with primer and barcode identifiers

DESCRIPTION

usage: MaskPrimers.py [--version] [-h] ...

Removes primers and annotates sequences with primer and barcode identifiers

help:

show program's version number and exit
show this help message and exit

subcommands:

Alignment method
Find primer matches using pairwise local alignment.
Find primer matches by scoring primers at a fixed position.
Remove and annotate a fixed sequence region.

output files:

mask-pass
processed reads with successful primer matches.
mask-fail
raw reads failing primer identification.

output annotation fields:

SEQORIENT
the orientation of the output sequence. Either F (input) or RC (reverse complement of input).
PRIMER
name of the best primer match.
BARCODE
the sequence preceding the primer match. Only output when the --barcode flag is specified.

AUTHOR


This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.

May 2020 MaskPrimers.py 0.6.0