malt-build(1)
Index builder for MALT (MEGAN alignment tool)
Description
MALT-BUILD
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)