Scroll to navigation

MAPSEMBLER2_EXTREMITIES(1) User Commands MAPSEMBLER2_EXTREMITIES(1)

NAME

mapsembler2_extremities - performs the first step of Mapsembler2_extend

SYNOPSIS

mapsembler2_extremities --k <kmersize> --starters <fasta> --reads <dataset> --output <substarterfile> [optional arguments]

DESCRIPTION

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

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
October 2018 mapsembler2_extremities 2.2.4