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.