essaMEM is an algorithm for calculating maximal exact matches using enhanced sparse suffix arrays

Installing: 1 go to the folder that contains the essaMEM.tgz file type the following: tar -xvzf essaMEM.tgz cd essaMEM make

Usage: ./mummer [options] <query-file1, query-file2, ...>

Implemented MUMmer v3 options: -mum compute maximal matches that are unique in both sequences -mumreference compute maximal matches that are unique in the reference- sequence but not necessarily in the query-sequence (default) -mumcand same as -mumreference -maxmatch compute all maximal matches regardless of their uniqueness -l set the minimum length of a match if not set, the default value is 20 -b compute forward and reverse complement matches -F force 4 column output format regardless of the number of reference sequence inputs -n match only the characters a, c, g, or t -L print length of query sequence in header of matches -r compute only reverse complement matches -s print first 53 characters of the matching substring -c report the query position of a reverse complement match relative to the forward strand of the query sequence

Additional options: -k sampled suffix positions (one by default) -threads number of threads to use for -maxmatch, only valid k > 1 -qthreads number of threads to use for queries -suflink use suffix links (1=yes or 0=no) in the index and during search [auto] -child use child table (1=yes or 0=no) in the index and during search [auto] -skip sparsify the MEM-finding algorithm even more, performing jumps of skip*k [auto (l-10)/k] this is a performance parameter that trade-offs SA traversal with checking of right-maximal MEMs

Example usage:

./mummer -maxmatch -l 20 -b -n -k 3 -threads 3 ref.fa query.fa Find all maximal matches on forward and reverse strands of length 20 or greater, matching only a, c, t, or g. Index every 3rd position in the ref.fa and use 3 threads to find MEMs. Fastest method for one long query sequence.

./mummer -maxmatch -l 20 -b -n -k 3 -qthreads 3 ref.fa query.fa Same as above, but now use a single thread for every query sequence in query.fa. Fastest for many small query sequences.