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e-mem - finds position and length of all Maximal Exact Matches (MEMs) for very

E-MEM(1) User Commands E-MEM(1)

NAME

e-mem - finds position and length of all Maximal Exact Matches (MEMs) for very large genomes

SYNOPSIS

e-mem [ options] <reference-file> <query-file>

DESCRIPTION

e-mem finds and outputs the position and length of all maximal exact matches (MEMs) between <query-file> and <reference-file>

OPTIONS

-n
match only the characters a, c, g, or t they can be in upper or in lower case
-l
set the minimum length of a match. The default length is 50
-b
compute forward and reverse complement matches
-r
only compute reverse complement matches
-c
report the query-position of a reverse complement match relative to the original query sequence
-F
force 4 column output format regardless of the number of reference sequence input
-L
show the length of the query sequences on the header line
-d
set the split size. The default value is 1
-t
number of threads. The default is 1 thread
-h
show 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.
May 2017 e-mem 0.0+20160706