MALT-BUILD(1)

🦋 malt-build — the index builder bestie 💅

okay so you want to meet malt-build? it's the User Commands girlie from the MALT-BUILD(1) manual, and she's literally the Index builder for MALT (MEGAN alignment tool). no cap. she takes your reference files and turns them into a whole ✨index✨. slay.

🌸 SYNOPSIS 🌸

malt-build [options]

💖 DESCRIPTION 💖

BUilds an index for MALT (MEGAN alignment tool). that's the whole job, bestie. she builds. you run her. iconic.

✨ OPTIONS ✨

🎀 Input:

• -i, --input [string(s)] — Input reference file(s). Mandatory option. like, you have to give her these, fr fr.
• -s, --sequenceType [string] — Sequence type. Mandatory option. Legal values: DNA, Protein. pick one, she's not a mind reader 🫶

🌈 Output:

• -d, --index [string] — Name of index directory. Mandatory option. yes bestie, another mandatory one. she needs somewhere to put the index 💖

🔥 Performance:

• -t, --threads [number] — Number of worker threads. Default value: 8.
• -st, --step [number] — Step size to advance seed. values greater than 1 reduce index size and sensitivity. Default value: 1. so like, bigger step = smaller index but you lose sensitivity. tradeoffs, babe 😭

🌱 Seed:

• -ss, --shapes [string(s)] — Seed shape(s). Default value(s): default.
• -mh, --maxHitsPerSeed [number] — Maximum number of hits per seed. Default value: 1000.
• -pr, --proteinReduct [string] — Name or definition of protein alphabet reduction (BLOSUM50_10,BLOSUM50_11,BLOSUM50_15,BLOSUM50_4,BLOSUM50_8,DIAMOND_11,GBMR4,HSDM17,MALT_10,SDM12,UNREDUCED). Default value: DIAMOND_11.

🧚 Classification:

• -c, --classify [string(s)] — Classifications (any of EGGNOG INTERPRO2GO KEGG SEED Taxonomy). Mandatory option. yeah. mandatory. again. she's thorough 💅
• -g2eggnog, --gi2eggnog [string] — GI-to-EGGNOG mapping file.
• -r2eggnog, --ref2eggnog [string] — RefSeq-to-EGGNOG mapping file.
• -s2eggnog, --syn2eggnog [string] — Synonyms-to-EGGNOG mapping file.
• -g2interpro2go, --gi2interpro2go [string] — GI-to-INTERPRO2GO mapping file.
• -r2interpro2go, --ref2interpro2go [string] — RefSeq-to-INTERPRO2GO mapping file.
• -s2interpro2go, --syn2interpro2go [string] — Synonyms-to-INTERPRO2GO mapping file.
• -g2kegg, --gi2kegg [string] — GI-to-KEGG mapping file.
• -r2kegg, --ref2kegg [string] — RefSeq-to-KEGG mapping file.
• -s2kegg, --syn2kegg [string] — Synonyms-to-KEGG mapping file.
• -g2seed, --gi2seed [string] — GI-to-SEED mapping file.
• -r2seed, --ref2seed [string] — RefSeq-to-SEED mapping file.
• -s2seed, --syn2seed [string] — Synonyms-to-SEED mapping file.
• -g2taxonomy, --gi2taxonomy [string] — GI-to-Taxonomy mapping file.
• -r2taxonomy, --ref2taxonomy [string] — RefSeq-to-Taxonomy mapping file.
• -s2taxonomy, --syn2taxonomy [string] — Synonyms-to-Taxonomy mapping file.
• -tn, --parseTaxonNames — Parse taxon names. Default value: true.
• -gif, --geneInfoFile [string] — File containing gene information.

🍓 Other:

• -fwo, --firstWordOnly — Save only first word of reference header. Default value: false.
• -rns, --random [number] — Random number generator seed. Default value: 666. 😭 not the number bestie
• -hsf, --hashScaleFactor [number] — Hash table scale factor. Default falue: 0.9.
• -v, --verbose — Echo commandline options and be verbose. Default value: false.
• -h, --help — Show program usage and quit.

👑 AUTHOR(s) 👑

Daniel H. Huson. we stan 🫶

🌟 SEE ALSO 🌟

malt-run(1) — go read that one next bestie, iykyk 💜

okay that's the whole vibe check! this page is from malt-build, dated January 2022, and it lives in the MALT-BUILD(1) manual section. periodt 💅✨