.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH LASTZ "1" "June 2020" "lastz 1.04.03" "User Commands"
.SH NAME
lastz \- pairwise aligning DNA sequences
.P
lastz_D \- pairwise aligning DNA sequences with double-float scoring
.SH DESCRIPTION
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.
.SH OPTIONS
.TP
target[[start..end]]
spec/file containing target sequence (fasta, fastq,
nib, 2bit or hsx);  [start..end] defines a subrange of
the file
(use \fB\-\-help\fR=\fI\,files\/\fR for more details)
.TP
query[[start..end]]
spec/file containing query sequences;  if absent,
queries come from stdin (if needed)
.TP
\fB\-\-self\fR
the target sequence is also the query
(this replaces the query file)
.TP
\fB\-\-seed\fR=\fI\,match\/\fR<length>
use a word with no gaps instead of a seed pattern
.TP
\fB\-\-[no]transition\fR[=\fI\,2\/\fR]
allow one or two transitions in a seed hit
(by default a transition is allowed)
.TP
\fB\-\-step=\fR<length>
set step length (default is 1)
.TP
\fB\-\-strand\fR=\fI\,both\/\fR
search both strands
.TP
\fB\-\-strand\fR=\fI\,plus\/\fR
search + strand only (matching strand of query spec)
.TP
\fB\-\-strand\fR=\fI\,minus\/\fR
search \- strand only (opposite strand of query spec)
(by default both strands are searched)
.TP
\fB\-\-ambiguous\fR=\fI\,n[\/\fR,<penalty>] treat N as an ambiguous nucleotide
(by default N is treated as a sequence splicing
.IP
character)
.TP
\fB\-\-ambiguous\fR=\fI\,iupac[\/\fR,<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
.IP
is rejected)
.TP
\fB\-\-[no]gfextend\fR
perform gap\-free extension of seed hits to HSPs
(by default extension is performed)
.TP
\fB\-\-[no]chain\fR
perform chaining
.TP
\fB\-\-chain=\fR<diag,anti>
perform chaining with given penalties for diagonal and
anti\-diagonal
(by default no chaining is performed)
.TP
\fB\-\-[no]gapped\fR
perform gapped alignment (instead of gap\-free)
(by default gapped alignment is performed)
.TP
\fB\-\-notrivial\fR
do not output a trivial self\-alignment block if the
target and query happen to be identical
.TP
\fB\-\-scores=\fR<file>
read substitution scores from a file
(default is HOXD70)
.TP
\fB\-\-match=\fR<R>,<P>
scores are +R/\-P for match/mismatch
.TP
\fB\-\-gap=\fR<open,extend>
set gap open and extend penalties (default is 400,30)
.TP
\fB\-\-xdrop=\fR<score>
set x\-drop threshold (default is 10*sub[A][A])
.TP
\fB\-\-ydrop=\fR<score>
set y\-drop threshold (default is open+300extend)
.TP
\fB\-\-noxtrim\fR
if x\-drop extension encounters end of sequence, don't
trim back to peak score (use this for short reads)
.TP
\fB\-\-noytrim\fR
if y\-drop extension encounters end of sequence, don't
trim back to peak score (use this for short reads)
.TP
\fB\-\-hspthresh=\fR<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
.TP
\fB\-\-exact=\fR<length>
set threshold for exact matches
if specified, exact matches are found rather than high
scoring pairs (replaces \fB\-\-hspthresh\fR)
.TP
\fB\-\-inner=\fR<score>
set threshold for HSPs during interpolation
(default is no interpolation)
.TP
\fB\-\-gappedthresh=\fR<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 \fB\-\-hspthresh\fR)
.TP
\fB\-\-[no]entropy\fR
involve entropy in filtering high scoring pairs
(default is "entropy")
.TP
\fB\-\-nomirror\fR
don't report mirror\-image alignments when using \fB\-\-self\fR
(default is to skip processing them, but recreate them
in the output)
.TP
\fB\-\-allocate\fR:traceback=<bytes>
space for trace\-back information
(default is 80.0M)
.TP
\fB\-\-masking=\fR<count>
mask any position in target hit this many times
zero indicates no masking
(default is no masking)
.TP
\fB\-\-identity=\fR<min>[..<max>] filter alignments by percent identity
0<=min<=max<=100;  blocks (or HSPs) outside min..max
are discarded
(default is no identity filtering)
.TP
\fB\-\-coverage=\fR<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)
.TP
\fB\-\-output=\fR<file>
specify output alignment file;  otherwise alignments
are written to stdout
.TP
\fB\-\-format=\fR<type>
specify output format; one of lav, axt, maf, cigar,
rdotplot, text or general
(use \fB\-\-help\fR=\fI\,formats\/\fR for more details)
(by default output is LAV)
.TP
\fB\-\-rdotplot=\fR<file>
create an output file suitable for plotting in R.
.TP
\fB\-\-progress=\fR<n>
report processing of every nth query
.TP
\fB\-\-version\fR
report the program version and quit
.TP
\fB\-\-help\fR
list all options
.TP
\fB\-\-help\fR=\fI\,files\/\fR
list information about file specifiers
.TP
\fB\-\-help\fR=\fI\,formats\/\fR
list information about output file formats
.TP
\fB\-\-help\fR=\fI\,shortcuts\/\fR
list blastz\-compatible shortcuts
.TP
\fB\-\-help\fR=\fI\,defaults\/\fR
list scoring defaults for your current settings
.TP
\fB\-\-help\fR=\fI\,yasra\/\fR
list yasra\-specific shortcuts
.SH SEE ALSO
The preceding list is not comprehensive.  The most up\-to\-date list is
available at http://www.bx.psu.edu/~rsharris/lastz
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.