LAMBDA2_SEARCHN(1)

📦
version 2.0.1 · 5 versions
, in debian trixie, ubuntu questing

💖 lambda2_searchn — the Local Aligner for Massive Biological DatA 💖

okay bestie, buckle up, we're reading the manual for lambda2_searchn (that's the LAMBDA2_SEARCHN(1) page, section 1, general commands, iykyk) and honestly? it's giving main character energy. ✨

✨ SYNOPSIS ✨

lambda2 searchn [OPTIONS] -q QUERY.fasta -i INDEX.lambda [-o output.m8]

🦋 DESCRIPTION 🦋

Lambda is a local aligner optimized for many query sequences and searches in protein space. She's compatible with BLAST, but so much faster than BLAST and many other comparable tools. Not to be dramatic but it's literally not even close. 💅

Detailed information lives in the wiki: <https://github.com/seqan/lambda/wiki>

🎀 OPTIONS 🎀

  • -h, --help — shows you the help message. the bare minimum, the basics, we love her. 🫶
  • -hh, --full-help — shows the help message with advanced options. for when you're ready to unlock the secret menu. 👑
  • --version — prints version info. know who you're dealing with.
  • --copyright — prints the long copyright info. the whole legal saga.
  • -v, --verbosity INTEGER — how much diagnostic output she yaps while working: 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. yes she does the decompression for you, no you don't have to ask. 💖
  • -i, --index INPUT_DIRECTORY — the database index (created by the lambda mkindexn command). valid filetype is: .lambda.

🍓 Output Options

  • -o, --output OUTPUT_FILE — the file that holds reports on hits (.m* are blastall -m* formats; .m8 is tab-separated, .m9 is tab-separated 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.
  • --output-columns STRING — prints the specified column combination and/or order (.m8 and .m9 outputs only); call -oc help for more details. Default: std.
  • --percent-identity INTEGER — only outputs matches above this threshold (and this check happens before the e-value check, fyi). In range [0..100]. Default: 0.
  • -e, --e-value DOUBLE — only outputs matches that score below this threshold. In range [0..100]. Default: 1e-04.
  • --bit-score DOUBLE — only outputs matches that score above this threshold. In range [0..1000]. Default: 0.
  • -n, --num-matches INTEGER — prints at most this number of matches per query. In range [1..10000]. Default: 256.
  • --sam-with-refheader BOOL — BAM files require all subject names to be written to the header. For SAM this is not required, so Lambda does not automatically do it, to save space (especially for protein databases this is a LOT!). If you still want them with SAM — e.g. for better BAM compatibility — use this option. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: off.
  • --sam-bam-seq STRING — writes the matching DNA subsequence into the SAM/BAM file. 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 — writes the specified optional columns to the SAM/BAM file. Call --sam-bam-tags help for more details. Default: AS NM ae ai qf.
  • --sam-bam-clip STRING — whether to hard-clip or soft-clip the regions beyond the local match. Soft-clipping retains 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. Default: autodetected. she'll figure it out herself, she's smart like that.

🧚 Seeding / Filtration

  • --adaptive-seeding BOOL — grows the seed if it has too many hits (that's the low complexity filter, btw). One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: off.
  • --seed-length INTEGER — length of the seeds. In range [3..50]. Default: 14.
  • --seed-offset INTEGER — offset for seeding (if unset = seed-length/2). In range [1..50]. Default: 7.
  • --seed-delta INTEGER — maximum seed distance. In range [0..1]. Default: 1.
  • --seed-delta-increases-length BOOL — seed delta increases the min. seed length (for affected seeds). One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: off.
  • --seed-half-exact BOOL — allows errors only in the second half of the seed. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on.

💜 Miscellaneous Heuristics

  • --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..10]. Default: 2.
  • --pre-scoring-threshold DOUBLE — minimum average score per position in the pre-scoring region. In range [0..20]. Default: 2.
  • --filter-putative-duplicates BOOL — filters hits that will likely duplicate a match already found. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on.
  • --filter-putative-abundant BOOL — if the maximum number of matches per query are found already, stop searching if the remaining realm looks unfeasible. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on.
  • --merge-putative-siblings BOOL — merge seed from one region, stop searching if the remaining realm looks unfeasable. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on.

⭐ Scoring

  • --score-gap INTEGER — score per gap character. In range [-1000..1000]. Default: -2.
  • --score-gap-open INTEGER — additional cost for opening a gap. In range [-1000..1000]. Default: -5.
  • --score-match INTEGER — match score [only BLASTN]. In range [-1000..1000]. Default: 2.
  • --score-mismatch INTEGER — mismatch score [only BLASTN]. In range [-1000..1000]. Default: -3.

🔥 Extension

  • -x, --x-drop INTEGER — stop Banded extension if score x below the maximum seen (-1 means no xdrop). In range [-1..1000]. 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..1000]. Default: -3.
  • -m, --extension-mode STRING — choice of extension algorithms. One of auto, xdrop, and fullSerial. Default: auto.

👑 TUNING 👑

Tuning the seeding parameters and (de)activating alphabet reduction has a strong influence on both speed and sensitivity. We recommend the following alternative profiles for protein searches:

fast (high similarity):       --seed-delta-increases-length on

sensitive (lower similarity): --seed-offset 3

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

ngl bestie, if your search is being weird, it's probably the seeding. tune the seeds. always the seeds. 😭

lambda2 searchn Copyright: 2013-2019 Hannes Hauswedell, released under the GNU AGPL v3 (or later); 2016-2019 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.

fr fr, cite the paper. it's free real estate in your references section and it keeps the icons fed. 🫶

that's the whole page, no cap. this one's lambda2 searchn 2.0.1, dated Nov 28 2024 — and yes, the page itself lives under the name LAMBDA2_SEARCHN(1). slay, go align something. 💅✨🧬

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