LASTZ(1)

💖 LASTZ 💖

okay bestie, gather round, because today we're talking about lastz — the manual page for pairwise aligning DNA sequences. and there's a bonus twin: lastz_D, which does the exact same thing but with double-float scoring. two icons, one vibe. 🧬✨

🌸 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, no cap, and it's backward compatible with BLASTZ's command-line syntax. that means it supports all of BLASTZ's options but also has extra ones of its own, and it may produce slightly different alignment results. so like… same energy, slightly different output. slay but make it your own. 💅

✨ OPTIONS ✨

fr fr, here's the whole menu, every single one, no skips:

• target[[start..end]] — spec/file containing the 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 it's 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 (the matching strand of the query spec)
• --strand=minus — search - strand only (the opposite strand of the 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 the 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

🎀 SEE ALSO 🎀

ngl, the list above is not comprehensive. the most up-to-date list lives at http://www.bx.psu.edu/~rsharris/lastz — go check it, bestie. 🫶

👑 AUTHOR 👑

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

and that's the whole thing! this page is from lastz 1.04.03, dated June 2020, and it's the LASTZ(1) manual — User Commands section, in case you were wondering. mwah, take care of your sequences. 💖🧬✨