LAMBDA(1)

📦
version 1.0.3 · 2 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 NAME 💖

okay so welcome to the LAMBDA(1) manual bestie, pull up a chair 🫶 this whole page is about lambda — the Local Aligner for Massive Biological DatA. yes the acronym ate, we love a backronym moment. 💅

🦋 SYNOPSIS 🦋

lambda [OPTIONS] -q QUERY.fasta -d DATABASE.fasta [-o output.m8]

like. that's it. that's the whole vibe. 🌸

✨ DESCRIPTION ✨

Lambda is a local aligner built different — it's optimized for so many query sequences and for searching in protein space. 🧬✨ It's compatible with BLAST, but it's much faster than BLAST and a whole pile of other comparable tools. no cap, it's giving speed.

want the full tea? detailed info lives in the wiki: <https://github.com/seqan/lambda/wiki>

👑 OPTIONS 👑

the main-character flags. read them, love them, use them. 💅

  • -h, --help — displays the help message. the classic. 🫶
  • -hh, --full-help — displays the help message with the advanced options. for when you want the extended cut. ✨
  • --version-check BOOL — turn this off to disable the app's version update notifications. one of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: 1.
  • --version — displays version information. slay.
  • --copyright — displays the long copyright information. the receipts, basically. 📜
  • -v, --verbosity INTEGER — display more/less diagnostic output while it's running: 0 [only errors]; 1 [default]; 2 [+run-time, options and statistics]. in range [0..2]. Default: 1.

📥 Input Options 📥

  • -q, --query INPUT_FILE — your query sequences. valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression. so many options and honestly? iconic. 🌈
  • -d, --database INPUT_FILE — path to the original database sequences. ⚠️ heads up bestie: a precomputed index with .sa or .fm needs to exist! like fr fr, it's not optional. valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.
  • -di, --db-index-type STRING — the database index is in this format. one of sa and fm. Default: fm.

📤 Output Options 📤

  • -o, --output OUTPUT_FILE — the file that holds the reports on hits (.m* are blastall -m* formats; .m8 is tab-seperated, .m9 is tab-seperated with with comments, .m0 is pairwise format). valid filetypes are: .sam[.*], .m9[.*], .m8[.*], .m0[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression. Default: output.m8.
  • -oc, --output-columns STRING — print the specified column combination and/or order (.m8 and .m9 outputs only); call -oc help for more details. Default: std.
  • -id, --percent-identity INTEGER — only output matches above this threshold (this gets checked before the e-value check, fyi). in range [0..100]. Default: 0.
  • -e, --e-value DOUBLE — only output matches that score below this threshold. in range [0..inf]. Default: 0.1.
  • -nm, --num-matches INTEGER — print at most this many matches per query. in range [1..inf]. Default: 500.
  • --sam-with-refheader STRING — BAM files require all subject names to be written to the header. for SAM that's not required, so Lambda doesn't automatically do it, to save space (and for a protein database that is a lot of space!). if you still want them with SAM — like for better BAM compatibility — use this option. one of on and off. Default: off.
  • --sam-bam-seq STRING — write the matching DNA subsequence into the SAM/BAM file (BLASTN). for BLASTX and TBLASTX the matching protein sequence is "untranslated" and the positions get retransformed to the original sequence. for BLASTP and TBLASTN there is no DNA sequence, so a * gets written to the SEQ column. the matching protein sequence can be written as an optional tag, see --sam-bam-tags. if set to uniq then the sequence is omitted iff it is identical to the previous match's subsequence. one of always, uniq, and never. Default: uniq.
  • --sam-bam-tags STRING — write the specified optional columns to the SAM/BAM file. call --sam-bam-tags help for more details. Default: AS NM ZE ZI ZF.
  • --sam-bam-clip STRING — whether to hard-clip or soft-clip the regions beyond the local match. soft-clipping keeps the full sequence in the output file, but obviously uses more space. one of hard and soft. Default: hard.

⚙️ General Options ⚙️

  • -t, --threads INTEGER — number of threads to run concurrently. go faster bestie 🏃‍♀️
  • -qi, --query-index-type STRING — controls double-indexing. one of radix and none. Default: none.

🔤 Alphabets and Translation 🔤

  • -p, --program STRING — Blast Operation Mode. one of blastn, blastp, blastx, tblastn, and tblastx. Default: blastx.
  • -g, --genetic-code INTEGER — the translation table to use for nucl -> amino acid translation (not for BlastN, BlastP). see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c for ids (default is generic). six frames are generated. Default: 1.
  • -ar, --alphabet-reduction STRING — Alphabet Reduction for the seeding phase (ignored for BLASTN). one of none and murphy10. Default: murphy10.

🌱 Seeding / Filtration 🌱

  • -sl, --seed-length INTEGER — length of the seeds (default = 14 for BLASTN). Default: 10.
  • -so, --seed-offset INTEGER — offset for seeding (if unset = seed-length, non-overlapping; default = 5 for BLASTN). Default: 10.
  • -sd, --seed-delta INTEGER — maximum seed distance. Default: 1.

🔮 Miscellaneous Heuristics 🔮

  • -ps, --pre-scoring INTEGER — evaluate the score of a region NUM times the size of the seed before extension (0 -> no pre-scoring, 1 -> evaluate seed, n -> area around seed, as well; default = 1 if no reduction is used). in range [1..inf]. Default: 2.
  • -pt, --pre-scoring-threshold DOUBLE — minimum average score per position in the pre-scoring region. Default: 2.
  • -pd, --filter-putative-duplicates STRING — filter hits that will likely duplicate a match already found. one of on and off. Default: on.
  • -pa, --filter-putative-abundant STRING — if the maximum number of matches per query are found already, stop searching if the remaining realm looks unfeasable. one of on and off. Default: on.

🎯 Scoring 🎯

  • -sc, --scoring-scheme INTEGER — use '45' for Blosum45; '62' for Blosum62 (default); '80' for Blosum80; [ignored for BlastN]. Default: 62.
  • -ge, --score-gap INTEGER — score per gap character (default = -2 for BLASTN). Default: -1.
  • -go, --score-gap-open INTEGER — additional cost for opening a gap (default = -5 for BLASTN). Default: -11.
  • -ma, --score-match INTEGER — match score [only BLASTN]. Default: 2.
  • -mi, --score-mismatch INTEGER — mismatch score [only BLASTN]. Default: -3.

🚀 Extension 🚀

  • -x, --x-drop INTEGER — stop Banded extension if the score is x below the maximum seen (-1 means no xdrop). in range [-1..inf]. Default: 30.
  • -b, --band INTEGER — size of the DP-band used in extension (-3 means log2 of query length; -2 means sqrt of query length; -1 means full dp; n means band of size 2n+1). in range [-3..inf]. Default: -3.

🌟 TUNING 🌟

okay so real talk: tuning the seeding parameters and (de)activating alphabet reduction has a strong influence on both speed and sensitivity. we recommend these alternative profiles for protein searches, bestie:

  • fast (high similarity): -ar none -sl 7 -sd 0
  • sensitive (lower similarity): -so 5

for further information see the wiki: <https://github.com/seqan/lambda/wiki>

the serious part. still cute, but serious. 💜

lambda Copyright: 2013-2017 Hannes Hauswedell, released under the GNU GPL v3 (or later); 2016-2017 Knut Reinert and Freie Universität Berlin, released under the 3-clause-BSDL

SeqAn Copyright: 2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.

in your academic works please cite: Hauswedell et al (2014); doi: 10.1093/bioinformatics/btu439

for full copyright and/or warranty information see --copyright.

and that's the whole page, bestie 🎀 this was lambda 1.0.2, dated Feb 8 2020 — go align something massive and slay. 💖✨🦋

📦 where this page comes from