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.