MALT-RUN(1)

💅 MALT-RUN(1) — the bestie guide 💅

User Commands · MALT-RUN · like, the coolest aligner page you'll ever read ✨

---

🌸 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. (yes bestie, THE author, iconic behavior 👑)

---

🔍 SEE ALSO 🔍

malt-build(1)

---

And that's the whole vibe, fr fr — this page was written by malt-run back in January 2022 and it's still serving looks. slay, go align something. 💖✨🎀