LAMBDA_INDEXER(1)

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

🦋 LAMBDA_INDEXER — okay bestie, let's build you a database 💅

So this is lambda_indexer, bestie. It's the indexer for making lambda-compatible databases. The manual calls it lambda_indexer(1), and honestly? Iconic. Let's go. ✨

🌸 SYNOPSIS

lambda_indexer [OPTIONS] -d DATABASE.fasta

That's it. That's the whole vibe. Give it options, give it a database, it does the thing. 🫶

💖 DESCRIPTION

Okay so listen. Lambda is a local aligner that's built different — it's optimized for when you have so many query sequences and you're searching in protein space. It's compatible with BLAST, but it's much faster than BLAST and honestly faster than a lot of other comparable tools too. No cap. 🔥

Detailed info lives in the wiki, and you should lowkey go read it:

<https://github.com/seqan/lambda/wiki>

And this thing right here? This is the indexer binary for creating lambda-compatible databases. It's the pre-game. It's the getting-ready-with-you-in-the-bathroom part of the process. 💅

✨ OPTIONS ✨

🎀 The basics

  • -h, --help — shows you the help message. classic.
  • -hh, --full-help — shows the help message with the advanced options. the director's cut, the extended edition. 👑
  • --version-check BOOL — turn this OFF if you don't want the app bugging you about version updates. Accepts one of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: 1.
  • --version — displays version info. slay.
  • --copyright — displays the long copyright information. grab a snack. 🍓
  • -v, --verbosity INTEGER — how much diagnostic output you get while it's working: 0 [only errors]; 1 [default]; 2 [+run-time, options and statistics]. Has to be in range [0..2]. Default: 1.

📂 Input Options

  • -d, --database INPUT_FILE — your database sequences. this is the main character. 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 bestie, it unzips for you, it's so thoughtful. 🧚
  • -s, --segfile INPUT_FILE — SEG intervals for the database (optional). Valid filetype is: .seg.

💾 Output Options

  • -di, --db-index-type STRING — suffix array or full-text minute space. One of sa and fm. Default: fm.
  • --truncate-ids STRING — truncates IDs at the first whitespace. This saves a lot of space, and it's irrelevant for all LAMBDA output formats other than BLAST Pairwise (.m0). One of on and off. Default: on.

🧬 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 (not for BlastN, BlastP). See <https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c> for ids (default is generic). Default: 1.
  • -ar, --alphabet-reduction STRING — Alphabet Reduction for the seeding phase (ignored for BLASTN). One of none and murphy10. Default: murphy10.

⚙️ Algorithm

  • -a, --algorithm STRING — algorithm for SA construction (also used for FM; see Memory Requirements below!). One of mergesort, quicksortbuckets, quicksort, radixsort, and skew7ext. Default: radixsort.
  • -t, --threads INTEGER — number of threads to run concurrently (ignored if a == skew7ext).
  • -td, --tmp-dir STRING — temporary directory used by skew, defaults to working directory.

🌈 REMARKS

Please go look at the wiki (<https://github.com/seqan/lambda/wiki>) for more info on which indexes to choose and which algorithms to pick. pick wisely bestie, this is a vibe check moment. 🙈

⚠️ Note that the indexes created are binary and not compatible between different CPU endiannesses. Also the on-disk format is still subject to change between Lambda versions. so like, don't get too attached to your index files, they might ghost you between versions. 💀

lambda_indexer 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_indexer version 1.0.2, dated Feb 8 2020, and you found it in section LAMBDA_INDEXER(1). now go index something and be iconic. periodt. 💅✨

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