MaskPrimers.py1
Removes primers and annotates sequences with primer and barcode identifiers
Overview
usage: MaskPrimers.py [--version] [-h] ...
Removes primers and annotates sequences with primer and barcode identifiers
help:
-
--version -
show program's version number and exit
-
-h, --help -
show this help message and exit
subcommands:
|
Alignment method |
|
align
|
Find primer matches using pairwise local alignment. |
score
|
Find primer matches by scoring primers at a fixed position. |
extract
|
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
--barcodeflag is specified.
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).