LAMBDA2_MKINDEXP(1)

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

💖 NAME 💖

lambda2_mkindexp — the Local Aligner for Massive Biological DatA. That's the name bestie, and this whole page is LAMBDA2_MKINDEXP(1), section 1, no cap. 🫶

🌸 SYNOPSIS 🌸

lambda2 mkindexp [OPTIONS] -d DATABASE.fasta [-i INDEX.lambda]

✨ DESCRIPTION ✨

So, Lambda is a local aligner that's been optimized for when you've got a bajillion query sequences and you're searching in protein space. 🧬 It's compatible with BLAST — like, they can hang out together — but it is much faster than BLAST and honestly than a lot of other tools in the same lane. It's giving main character energy and it's earned it. 👑

If you want the detailed tea, it's all in the wiki: <https://github.com/seqan/lambda/wiki> 🌈

And what is this binary specifically? It's the indexer_binary — the one that makes lambda-compatible databases. So like, you build the index here first, then you go align. That's the whole vibe check. 💅

🎀 OPTIONS 🎀

  • -h, --help — shows you the help message. The basics, the quick rundown. 🌸
  • -hh, --full-help — shows you the help message with the advanced options. The deep lore. 🔥
  • --version — prints out version info. ✨
  • --copyright — prints out the long copyright information. The whole legal saga. 📜
  • -v, --verbosity INTEGER — how much diagnostic output you want during operation: 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 — the database 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. Literally so many options, pick your fighter. 🍓
  • -m, --acc-tax-map INPUT_FILE — an NCBI or UniProt accession-to-taxid mapping file. Download it from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/ or ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/. Valid filetypes are: .dat[.*] and .accession2taxid[.*], where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression. 🦋
  • -x, --tax-dump-dir INPUT_DIRECTORY — a directory that contains nodes.dmp and names.dmp; these get unzipped from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz. 💜

💫 Output Options

  • -i, --index OUTPUT_DIRECTORY — the output directory for the index files (defaults to "DATABASE.lambda"). Valid filetype is: .lambda. This is where the magic gets written down bestie. 🎀
  • --db-index-type STRING — suffix array or full-text minute space. One of fm and bifm. Default: fm. 👑
  • --truncate-ids BOOL — truncate IDs at first whitespace. This saves a lot of space and is irrelevant for all LAMBDA output formats other than BLAST Pairwise (.m0). One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on. ✨

🌈 Alphabets and Translation

  • -a, --input-alphabet STRING — alphabet of the database sequences (specify this to override auto-detection); if input is Dna, it will be translated. One of auto, dna5, and aminoacid. Default: auto. 🧬
  • -g, --genetic-code INTEGER — the translation table to use if input is Dna. See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c for ids (default is generic). Default: 1. 💖
  • -r, --alphabet-reduction STRING — alphabet reduction for the seeding phase. One of none and murphy10. Default: murphy10. 🌸

⭐ Algorithm

  • --algorithm STRING — the algorithm for SA construction (also used for FM; see Memory Requirements below — and yes, the ! is doing a lot of work there). One of mergesort, quicksortbuckets, quicksort, radixsort, and skew7ext. Default: radixsort. 🔥
  • -t, --threads INTEGER — number of threads to run concurrently. Default: autodetected. Let it cook. 💅
  • --tmp-dir OUTPUT_DIRECTORY — temporary directory used by skew, defaults to working directory. 🧚

💀 REMARKS 💀

Please see the wiki (<https://github.com/seqan/lambda/wiki>) for more info on which indexes to choose and which algorithms to pick. Choosing is a whole thing, and the wiki has the answers, fr fr. 🫶

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 assume it'll just work forever, bestie. 😭
  • lambda2 mkindexp 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.

Okay that's the whole page bestie!! This is lambda2 mkindexp version 2.0.1, and it was dated Nov 28 2024 — so when you cite it, you know exactly which one you mean. Go build those indexes, you're gonna slay. 💖✨🎀🦋🌸

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