lastz - pairwise aligning DNA sequences

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.

lastz 1.04.03                                       June 2020                                           LASTZ(1)

       LASTZ  is a drop-in replacement for BLASTZ, and is backward compatible with BLASTZ’s command-line syntax.
       That is, it supports all of BLASTZ’s options but also has  additional  ones,  and  may  produce  slightly
       different alignment results.

       lastz - pairwise aligning DNA sequences

       lastz_D - pairwise aligning DNA sequences with double-float scoring

       target[[start..end]]
              spec/file  containing  target  sequence  (fasta, fastq, nib, 2bit or hsx);  [start..end] defines a
              subrange of the file (use --help=files for more details)

       query[[start..end]]
              spec/file containing query sequences;  if absent, queries come from stdin (if needed)

       --self the target sequence is also the query (this replaces the query file)

       --seed=match<length>
              use a word with no gaps instead of a seed pattern

       --[no]transition[=2]
              allow one or two transitions in a seed hit (by default a transition is allowed)

       --step=<length>
              set step length (default is 1)

       --strand=both
              search both strands

       --strand=plus
              search + strand only (matching strand of query spec)

       --strand=minus
              search - strand only (opposite strand of query spec) (by default both strands are searched)

       --ambiguous=n[,<penalty>] treat N as an ambiguous nucleotide
              (by default N is treated as a sequence splicing

              character)

       --ambiguous=iupac[,<penalty>] treat any ambiguous IUPAC-IUB character as a
              completely ambiguous nucleotide (by default any sequence file with B,D,H,K,M,R,S,V,W,Y

              is rejected)

       --[no]gfextend
              perform gap-free extension of seed hits to HSPs (by default extension is performed)

       --[no]chain
              perform chaining

       --chain=<diag,anti>
              perform chaining with given penalties for diagonal and anti-diagonal (by default  no  chaining  is
              performed)

       --[no]gapped
              perform gapped alignment (instead of gap-free) (by default gapped alignment is performed)

       --notrivial
              do not output a trivial self-alignment block if the target and query happen to be identical

       --scores=<file>
              read substitution scores from a file (default is HOXD70)

       --match=<R>,<P>
              scores are +R/-P for match/mismatch

       --gap=<open,extend>
              set gap open and extend penalties (default is 400,30)

       --xdrop=<score>
              set x-drop threshold (default is 10*sub[A][A])

       --ydrop=<score>
              set y-drop threshold (default is open+300extend)

       --noxtrim
              if  x-drop extension encounters end of sequence, don't trim back to peak score (use this for short
              reads)

       --noytrim
              if y-drop extension encounters end of sequence, don't trim back to peak score (use this for  short
              reads)

       --hspthresh=<score>
              set  threshold  for  high  scoring  pairs  (default is 3000) ungapped extensions scoring lower are
              discarded <score> can also be a percentage or base count

       --exact=<length>
              set threshold for exact matches if specified, exact matches are found  rather  than  high  scoring
              pairs (replaces --hspthresh)

       --inner=<score>
              set threshold for HSPs during interpolation (default is no interpolation)

       --gappedthresh=<score> set threshold for gapped alignments
              gapped  extensions  scoring  lower  are  discarded  <score> can also be a percentage or base count
              (default is to use same value as --hspthresh)

       --[no]entropy
              involve entropy in filtering high scoring pairs (default is "entropy")

       --nomirror
              don't report mirror-image alignments when using --self (default is to skip  processing  them,  but
              recreate them in the output)

       --allocate:traceback=<bytes>
              space for trace-back information (default is 80.0M)

       --masking=<count>
              mask any position in target hit this many times zero indicates no masking (default is no masking)

       --identity=<min>[..<max>] filter alignments by percent identity
              0<=min<=max<=100;   blocks  (or  HSPs)  outside  min..max  are  discarded  (default is no identity
              filtering)

       --coverage=<min>[..<max>] filter alignments by percentage of query covered
              0<=min<=max<=100;  blocks (or HSPs) outside min..max are discarded (default is no  query  coverage
              filtering)

       --output=<file>
              specify output alignment file;  otherwise alignments are written to stdout

       --format=<type>
              specify  output format; one of lav, axt, maf, cigar, rdotplot, text or general (use --help=formats
              for more details) (by default output is LAV)

       --rdotplot=<file>
              create an output file suitable for plotting in R.

       --progress=<n>
              report processing of every nth query

       --version
              report the program version and quit

       --help list all options

       --help=files
              list information about file specifiers

       --help=formats
              list information about output file formats

       --help=shortcuts
              list blastz-compatible shortcuts

       --help=defaults
              list scoring defaults for your current settings

       --help=yasra
              list yasra-specific shortcuts

       The  preceding   list   is   not   comprehensive.    The   most   up-to-date   list   is   available   at
       http://www.bx.psu.edu/~rsharris/lastz