---
name: "malt-run"
section: "1"
platform: "linux"
package: "malt"
version: "0.5.2-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/malt-run"
---

# malt-run(1)

Sequences aligner using MALT (MEGAN alignment tool)

## 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)](/malt-build/1.md)