mapsembler2_extremities1
Performs the first step of mapsembler2_extend
Usage
mapsembler2_extremities --k
<kmersize>
--starters
<fasta>
--reads
<dataset>
--output
<substarterfile>
[optional
arguments]
Overview
This modules performs the first step of Mapsembler2_extend. For each starter, it outputs a list of extremities of the starter (of length *k*) are found in the reads, up to 1 indel or mismatch.
Options
--k(1 arg):-
kmer size that will be used for mapsembler2 [default '']
--starters(1 arg):-
starters fasta file [default '']
--reads(1 arg):-
reads dataset file name. Several reads sets can be provided, surrounded by "'s and separated by a space (e.g.
--reads"reads1.fa reads2.fa") [default '']
--output(1 arg):-
output substarters file name [default '']
--min-solid-subkmer(1 arg):-
minimim abundance to keep a subkmer [default '3']
-debug(0 arg):-
debugging
-nb-cores(1 arg):-
number of cores [default '0']
-verbose(1 arg):-
verbosity level [default '1']
-help(0 arg):-
display help about possible options
Releases
5 releases since Debian 9 (Stretch); the text changed 1 time.
--k until Debian 9 (Stretch);
--output until Debian 9 (Stretch);
--reads until Debian 9 (Stretch);
--starters until Debian 9 (Stretch);
-debug until Debian 9 (Stretch);
-help until Debian 9 (Stretch);
-nb-cores until Debian 9 (Stretch);
-verbose until Debian 9 (Stretch).