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LASTZ(1) User Commands LASTZ(1)

NAME

lastz - pairwise aligning DNA sequences

lastz_D - pairwise aligning DNA sequences with double-float scoring

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.

OPTIONS

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)
spec/file containing query sequences; if absent, queries come from stdin (if needed)
the target sequence is also the query (this replaces the query file)
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)
set step length (default is 1)
search both strands
search + strand only (matching strand of query spec)
search - strand only (opposite strand of query spec) (by default both strands are searched)
(by default N is treated as a sequence splicing
character)
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
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)
do not output a trivial self-alignment block if the target and query happen to be identical
read substitution scores from a file (default is HOXD70)
scores are +R/-P for match/mismatch
set gap open and extend penalties (default is 400,30)
set x-drop threshold (default is 10*sub[A][A])
set y-drop threshold (default is open+300extend)
if x-drop extension encounters end of sequence, don't trim back to peak score (use this for short reads)
if y-drop extension encounters end of sequence, don't trim back to peak score (use this for short reads)
set threshold for high scoring pairs (default is 3000) ungapped extensions scoring lower are discarded <score> can also be a percentage or base count
set threshold for exact matches if specified, exact matches are found rather than high scoring pairs (replaces --hspthresh)
set threshold for HSPs during interpolation (default is no interpolation)
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")
don't report mirror-image alignments when using --self (default is to skip processing them, but recreate them in the output)
space for trace-back information (default is 80.0M)
mask any position in target hit this many times zero indicates no masking (default is no masking)
0<=min<=max<=100; blocks (or HSPs) outside min..max are discarded (default is no identity filtering)
0<=min<=max<=100; blocks (or HSPs) outside min..max are discarded (default is no query coverage filtering)
specify output alignment file; otherwise alignments are written to stdout
specify output format; one of lav, axt, maf, cigar, rdotplot, text or general (use --help=formats for more details) (by default output is LAV)
create an output file suitable for plotting in R.
report processing of every nth query
report the program version and quit
list all options
list information about file specifiers
list information about output file formats
list blastz-compatible shortcuts
list scoring defaults for your current settings
list yasra-specific shortcuts

SEE ALSO

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

AUTHOR


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

June 2020 lastz 1.04.03