NAME
malt-build - Index builder for MALT (MEGAN alignment tool)
DESCRIPTION
SYNOPSIS
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malt-build [options]
DESCRIPTION
-
BUilds an index for MALT (MEGAN alignment tool)
OPTIONS
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Input:
- -i, --input [string(s)]
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Input reference file(s). Mandatory option.
- -s, --sequenceType [string]
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Sequence type. Mandatory option. Legal values: DNA, Protein
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Output:
- -d, --index [string]
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Name of index directory. Mandatory option.
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Performance:
- -t, --threads [number]
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Number of worker threads. Default value: 8.
- -st, --step [number]
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Step size to advance seed, values greater than 1 reduce index size and sensitivity. Default value: 1.
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Seed:
- -ss, --shapes [string(s)]
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Seed shape(s). Default value(s): default.
- -mh, --maxHitsPerSeed [number]
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Maximum number of hits per seed. Default value: 1000.
- -pr, --proteinReduct [string]
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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.
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Classification:
- -c, --classify [string(s)]
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Classifications (any of EGGNOG INTERPRO2GO KEGG SEED Taxonomy). Mandatory option.
- -g2eggnog, --gi2eggnog [string]
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GI-to-EGGNOG mapping file.
- -r2eggnog, --ref2eggnog [string]
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RefSeq-to-EGGNOG mapping file.
- -s2eggnog, --syn2eggnog [string]
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Synonyms-to-EGGNOG mapping file.
- -g2interpro2go, --gi2interpro2go [string]
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GI-to-INTERPRO2GO mapping file.
- -r2interpro2go, --ref2interpro2go [string]
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RefSeq-to-INTERPRO2GO mapping file.
- -s2interpro2go, --syn2interpro2go [string]
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Synonyms-to-INTERPRO2GO mapping file.
- -g2kegg, --gi2kegg [string]
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GI-to-KEGG mapping file.
- -r2kegg, --ref2kegg [string]
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RefSeq-to-KEGG mapping file.
- -s2kegg, --syn2kegg [string]
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Synonyms-to-KEGG mapping file.
- -g2seed, --gi2seed [string]
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GI-to-SEED mapping file.
- -r2seed, --ref2seed [string]
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RefSeq-to-SEED mapping file.
- -s2seed, --syn2seed [string]
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Synonyms-to-SEED mapping file.
- -g2taxonomy, --gi2taxonomy [string]
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GI-to-Taxonomy mapping file.
- -r2taxonomy, --ref2taxonomy [string]
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RefSeq-to-Taxonomy mapping file.
- -s2taxonomy, --syn2taxonomy [string]
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Synonyms-to-Taxonomy mapping file.
- -tn, --parseTaxonNames
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Parse taxon names. Default value: true
- -gif, --geneInfoFile [string]
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File containing gene information
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Other:
- -fwo, --firstWordOnly
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Save only first word of reference header. Default value: false.
- -rns, --random [number]
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Random number generator seed. Default value: 666.
- -hsf, --hashScaleFactor [number]
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Hash table scale factor. Default falue: 0.9.
- -v, --verbose
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Echo commandline options and be verbose. Default value: false.
- -h, --help
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Show program usage and quit.
AUTHOR(s)
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Daniel H. Huson.