Man page - malt-run(1)

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malt

Manual

MALT-RUN

NAME
DESCRIPTION
AUTHOR(s)
SEE ALSO

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 2ˆbits). 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.