Man page - malt-build(1)

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Package: malt
apt-get install malt

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malt

Manual

MALT-BUILD

NAME
DESCRIPTION
AUTHOR(s)
SEE ALSO

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.