set lower bound of sensitivity level for one-error matches (default 100)
-f, --forward
only compute forward matches
-r, --reverse
only compute reverse complement matches
-mN, --match-N
'N' matches with all other characters
-m, --max-hits NUM
output only NUM of the best hits (default 100)
-pa, --purge-ambiguous
purge reads with more than max-hits best matches
-lm, --low-memory
may decrease memory usage at the expense of runtime
-v, --verbose
verbose mode
-vv, --vverbose
very verbose mode
-V, --version
print version number
-h, --help
print this help
Output Format Options:
-a, --alignment
dump the alignment for each match
-gn, --genome-naming NUM
select how genomes are named
0 = use Fasta id (default)
1 = enumerate beginning with 1
-rn, --read-naming NUM
select how reads are named
0 = use Fasta id (default)
1 = enumerate beginning with 1
2 = use the read sequence (only for short reads!)
-so, --sort-order NUM
select how matches are sorted
0 = 1. read number, 2. genome position (default)
1 = 1. genome position, 2. read number
-pf, --position-format
0 = gap space (default)
1 = position space
AUTHOR
MicroRazerSwas written by Anne-Katrin Emde.
This manual page was generated using html2man and polished by
Soeren Sonnenburg <sonne@debian.org>, for the Debian project
(but may be used by others).