lastz1

Overview

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

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