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)