---
name: "malt-build"
section: "1"
platform: "linux"
package: "malt"
version: "0.5.2-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/malt-build"
---

# malt-build(1)

Index builder for MALT (MEGAN alignment tool)

## NAME

malt-build - Index builder for MALT (MEGAN alignment tool)

## DESCRIPTION

SYNOPSIS

-

  malt-build \[options\]

DESCRIPTION

-

  BUilds an index for MALT (MEGAN alignment tool)

OPTIONS

-

  Input:

- **-i**, **--input** \[string(s)\]

  Input reference file(s). Mandatory option.

- **-s**, **--sequenceType** \[string\]

  Sequence type. Mandatory option. Legal values: DNA, Protein

-

  Output:

- **-d**, **--index** \[string\]

  Name of index directory. Mandatory option.

-

  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.

-

  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.

- **-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.

- **-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.

## SEE ALSO

[**malt-run**(1)](/malt-run/1.md)