NAME

       malt-run - Sequences aligner using MALT (MEGAN alignment tool)

DESCRIPTION

       SYNOPSIS

              malt-run [options]

       DESCRIPTION

              Aligns sequences using MALT (MEGAN alignment tool)

       OPTIONS

              Mode:

       -m, --mode [string]
              Program  mode.  Mandatory  option.  Legal  values: Unknown, BlastN, BlastP, BlastX,
              Classifier

       -at, --alignmentType [string]
              Type of alignment to be  performed.  Default  value:  Local  Legal  values:  Local,
              SemiGlobal

              Input:

       -i, --inFile [string(s)]
              Input  file(s)  containing  queries  in  FastA  or  FastQ  format (gzip or zip ok).
              Mandatory option.

       -d, --index [string]
              Index directory as generated by malt-build. Mandatory option.

              Output:

       -o, --output [string(s)]
              Output RMA file(s) or directory or stdout.

       -iu, --includeUnaligned
              Include unaligned queries in RMA output file. Default value: false.

       -a, --alignments [string(s)]
              Output alignment file(s) or directory or stdout.

       -f, --format [string]
              Alignment output format. Default value: SAM Legal values: SAM, Tab, Text

       -za, --gzipAlignments
              Compress alignments using gzip. Default value: true.

       -ssc, --samSoftClip
              Use soft clipping in SAM files (BlastN mode only). Default value: false.

       -sps, --sparseSAM
              Produce sparse SAM format (smaller, faster, but only suitable for  MEGAN).  Default
              value: false.

       -oa, --outAligned [string(s)]
              Aligned reads output file(s) or directory or stdout.

       -zal, --gzipAligned
              Compress aligned reads output using gzip. Default value: true.

       -ou, --outUnaligned [string(s)]
              Unaligned reads output file(s) or directory or stdout.

       -zul, --gzipUnaligned
              Compress unaligned reads output using gzip. Default value: true.

              Performance:

       -t, --numThreads [number]
              Number of worker threads. Default value: 4.

       -mem, --memoryMode [string]
              Memory mode. Default value: load Legal values: load, page, map

       -mt, --maxTables [number]
              Set the maximum number of seed tables to use (0=all). Default value: 0.

       -rqc, --replicateQueryCache
              Cache results for replicated queries. Default value: false.

              Filter:

       -b, --minBitScore [number]
              Minimum bit score. Default value: 50.0.

       -e, --maxExpected [number]
              Maximum expected score. Default value: 1.0.

       -id, --minPercentIdentity [number]
              Minimum percent identity. Default value: 0.0.

       -mq, --maxAlignmentsPerQuery [number]
              Maximum number of alignments per query. Default value: 25.

       -mrf, --maxAlignmentsPerRef [number]
              Maximum number of (non-overlapping) alignments per reference. Default value: 1.

              BlastN parameters:

       -ma, --matchScore [number]
              Match score. Default value: 2.

       -mm, --mismatchScore [number]
              Mismatch score. Default value: -3.

       -la, --setLambda [number]
              Parameter Lambda for BLASTN statistics. Default value: 0.625.

       -K, --setK [number]
              Parameter K for BLASTN statistics. Default value: 0.41.

              BlastP and BlastX parameters:

       -psm, --subMatrix [string]
              Protein substitution matrix to use. Default value: BLOSUM62 Legal values: BLOSUM45,
              BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM90

              DNA query parameters:

       -fo, --forwardOnly
              Align query forward strand only. Default value: false.

       -ro, --reverseOnly
              Align query reverse strand only. Default value: false.

              LCA parameters:

       -top, --topPercent [number]
              Top percent value for LCA algorithm. Default value: 10.0.

       -supp, --minSupportPercent [number]
              Min support value for LCA algorithm  as  a  percent  of  assigned  reads  (0==off).
              Default value: 0.001.

       -sup, --minSupport [number]
              Min support value for LCA algorithm (overrides --minSupportPercent). Default value:
              0.

       -mpi, --minPercentIdentityLCA [number]
              Min percent identity used by LCA algorithm. Default value: 0.0.

       -mif, --useMinPercentIdentityFilterLCA
              Use percent identity assignment filter. Default value: false.

       -wlca, --weightedLCA
              Use the weighted LCA for taxonomic assignment. Default value: false.

       -lcp, --lcaCoveragePercent [number]
              Set the percent for the LCA to cover. Default value: 100.0.

       -mag, --magnitudes
              Reads have magnitudes (to be used in taxonomic  or  functional  analysis).  Default
              value: false.

       -cf, --conFile [string]
              File of contaminant taxa (one Id or name per line).

              Heuristics:

       -spf, --maxSeedsPerFrame [number]
              Maximum number of seed matches per offset per read frame. Default value: 100.

       -spr, --maxSeedsPerRef [number]
              Maximum number of seed matches per read and reference. Default value: 20.

       -sh, --seedShift [number]
              Seed shift. Default value: 1.

              Banded alignment parameters:

       -go, --gapOpen [number]
              Gap open penalty. Default value: 11.

       -ge, --gapExtend [number]
              Gap extension penalty. Default value: 1.

       -bd, --band [number]
              Band width/2 for banded alignment. Default value: 4.

              Other:

       -rqcb, --replicateQueryCacheBits [number]
              Bits used for caching replicate queries (size is then 2^bits). Default value: 20.

       -xP, --xPart
              Show part of the table in human readable form for debugging. Default value: false.

       -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-build(1)