Specify minimum length of matches (default: 0)

Compute forward matches (default: yes)

Compute reverse matches (default: no)

Compute matches on reverse strand (default: no)

Specify minimum length of seed (default: 0)

Specify maximal frequency of maximal exact matches in reference sequence (default: 0)

Extend seed to both sides using xdrop algorithm, optional parameter specifies sensitivity (default: 97)

Specify xdrop cutoff score (argument 0 means undefined). If undefined an optimal value is determined automatically depending on the error rate

Extend seed to both sides using greedy algorithm with trimming of waves, optional parameter specifies sensitivity (default: 97)

Specify minimum identity of matches as integer in the range from 70 to 99 (for xdrop and greedy extension) (default: 80)

Specify input index (default: undefined)

specify what information about the matches to display alignment: show alignment (possibly followed by =<number> to specify width of alignment columns, default is ) seed_in_algn: mark the seed in alignment polinfo: add polishing information for shown alignment seed: abbreviation for seed.len seed.s seed.q failed_seed: show the coordinates of a seed extension, which does not satisfy the filter conditions fstperquery: output only the first found match per query tabsep: separate columns by tabulator, instead of space as default blast: output matches in blast format 7 (tabular with comment lines; instead of gap opens, indels are displayed) gfa2: output matches in gfa2 format custom: output matches in custom format, i.e. no columns are pre-defined; all columns have to be specified by the user cigar: display cigar string representing alignment (no distinction between match and mismatch) cigarX: display cigar string representing alignment (distinction between match (=) and mismatch (X)) trace: display trace, i.e. a compact representation of an alignment (possibly followed by =<delta>) to specify the delta-value; default value of delta is 50 dtrace: display trace as differences; like trace, but instead of an absolute value x, report the difference delta-x. This leads to smaller numbers and thus a more compact representation s.len: display length of match on subject sequence s.seqnum: display sequence number of subject sequence subject id: display sequence description of subject sequence s.start: display start position of match on subject sequence s.end: display end position of match on subject sequence strand: display strand of match using symbols F (forward) and P (reverse complement) q.len: display length of match on query sequence q.seqnum: display sequence number of query sequence query id: display sequence description of query sequence q.start: display start position of match on query sequence q.end: display end position of match on query sequence alignment length: display length of alignment mismatches: display number of mismatches in alignment indels: display number of indels in alignment gap opens: display number of indels in alignment score: display score of match editdist: display unit edit distance identity: display percent identity of match seed.len: display length seed of the match seed.s: display start position of seed in subject seed.q: display start position of seed in query s.seqlen: display length of subject sequence in which match occurs q.seqlen: display length of query sequence in which match occurs evalue: display evalue bit score: display bit score

switch on evalue filtering of matches (optional argument specifies evalue threshold) (default: 10.000000)

scan index rather than map it to main memory (default: no)

be verbose (default: no)

display help and exit

display version information and exit