usage - readmapping/essaMEM GitHub Wiki
- pull the github repository
- make
go to the folder that contains the essaMEM.tgz file and type the following:
- tar -xvzf essaMEM.tgz
- cd essaMEM
- make
./mummer [options] <reference-file> <query-file1, query-file2, ...>
| -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 |
| -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.