LAMBDA2_MKINDEXN(1)

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

✨ lambda2_mkindexn ✨

okay bestie, welcome to the lambda2_mkindexn manual page, a.k.a. the Local Aligner for Massive Biological DatA indexer 💅 it lives in the LAMBDA2_MKINDEXN(1) corner of your manual and it is genuinely iconic.

🌸 SYNOPSIS 🌸

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

that's it. that's the whole vibe. you give it a database, you get an index, we move on 🦋

💖 DESCRIPTION 💖

so, Lambda is a local aligner optimized for many query sequences and searches in protein space. She's compatible with BLAST, but — and I cannot stress this enough — much faster than BLAST and many other comparable tools. not me hyping her up, it's literally in the docs 😌

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

and okay, real talk: this binary right here is the indexer_binary for creating lambda-compatible databases. she's the one who preps everything so the rest of the tool can eat 🔥

🎀 OPTIONS 🎀

  • -h, --help — Display the help message. quick lil "what do I do" moment ✨
  • -hh, --full-help — Display the help message with advanced options. the deluxe help, if you will 💅
  • --version — Display version information. who are you? what are you? 🦋
  • --copyright — Display long copyright information. the legal tea ☕
  • -v, --verbosity INTEGER — Display more/less diagnostic output during operation: 0 [only errors]; 1 [default]; 2 [+run-time, options and statistics]. In range [0..2]. Default: 1. so basically: how much does she yap at you while she works 🗣️

🌈 Input Options:

  • -d, --database INPUT_FILE — 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. so many formats, so little time, she accepts them all no cap 💖
  • -m, --acc-tax-map INPUT_FILE — An NCBI or UniProt accession-to-taxid mapping file. Download 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. go get your taxonomy bestie 🧚
  • -x, --tax-dump-dir INPUT_DIRECTORY — A directory that contains nodes.dmp and names.dmp; 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. your lil index home 🏠
  • --db-index-type STRING — Suffix array or full-text minute space. One of fm and bifm. Default: fm. pick your fighter ⚔️
  • --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. snip snip ✂️

🦋 Algorithm:

  • --algorithm STRING — Algorithm for SA construction (also used for FM; see Memory Requirements below!). One of mergesort, quicksortbuckets, quicksort, radixsort, and skew7ext. Default: radixsort. the way she has options 😌
  • -t, --threads INTEGER — number of threads to run concurrently. Default: autodetected. she'll figure out how many lil helpers she gets 🔥
  • --tmp-dir OUTPUT_DIRECTORY — temporary directory used by skew, defaults to working directory. skew needs a lil scratch pad 🍓

⭐ REMARKS ⭐

Please see the wiki (<https://github.com/seqan/lambda/wiki>) for more information on which indexes to chose and which algorithms to pick. genuinely, go read it, iykyk 🫶

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. bestie. BESTIE. do not assume your index travels well between machines or versions, it does NOT 💀

lambda2 mkindexn 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.

and that's the whole page, bestie 🎀 this was lambda2 mkindexn version 2.0.1, dated Nov 28 2024, out here doing the most for your massive biological data. periodt 💅✨🦋

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