Command Reference

Command-Line Parameter Reference

autoMito

autoMito performs one-step de novo assembly of organellar genomes from sequencing reads.

Usage: PMAT autoMito [-i INPUT] [-o OUTPUT] [-t SEQTYPE] [options]
Example:
       PMAT autoMito -i hifi.fastq.gz -o hifi_assembly -t hifi -m -T 8
       PMAT autoMito -i ont.fastq.gz -o ont_assembly -t ont -S nextdenovo -C canu -N nextdenovo
       PMAT autoMito -i clr.fastq.gz -o clr_assembly -t clr -S canu -C canu

Required options:
   -i, --input          Input sequence file (fasta/fastq)
   -o, --output         Output directory
   -t, --seqtype        Sequence type (hifi/ont/clr)

Optional options:
   -k, --kmer           Kmer size for estimating genome size (default: 31)
   -g, --genomesize     Genome size (g/m/k), skip genome size estimation if set
   -p, --task           Task type (0/1), skip error correction for ONT/CLR by selecting 0, otherwise 1 (default: 1)
   -G, --organelles     Genome organelles (mt/pt/all, default: mt)
   -x, --taxo           Specify the organism type (0/1/2), 0: plants, 1: animals, 2: Fungi (default: 0)
   -S, --correctsoft    Error correction software (canu/nextdenovo, default: nextdenovo)
   -C, --canu           Canu path
   -N, --nextdenovo     NextDenovo path
   -n, --cfg            Config file for nextdenovo (default: temprun.cfg)
   -F, --factor         Subsample factor (default: 1)
   -D, --subseed        Random number seeding when extracting subsets (default: 6)
   -K, --breaknum       Break long reads (>30k) with this (default: 20000)
   -I, --minidentity    Set minimum overlap identity (default: 90)
   -L, --minoverlaplen  Set minimum overlap length (default: 40)
   -T, --cpu            Number of threads (default: 8)
   -m, --mem            Keep sequence data in memory to speed up computation
   -r, --runassembly    Custom path to runAssembly (default: bin/runAssembly)
   -h, --help           Show this help message and exit

Parameter Guidelines

1. BLASTn: Ensure blastn is accessible in your system PATH (already included in PMAT_v2.2.0.sif).
2. NextDenovo Configuration (-n): If using NextDenovo for ONT/CLR error correction, providing a configuration file is optional; PMAT2 automatically generates a temporary config file if not specified.
3. Kmer Analysis (-k): For HiFi sequencing data (-t hifi), kmer frequency and genome size estimation are automatically skipped.
4. In-Memory Acceleration (-m): Caches sequence subsets in memory to reduce disk I/O and accelerate assembly.
5. Overlap Identity (-I): Default is 90%. In complex repeat-rich genomes, increasing this value can help untangle repeat junctions.
6. Overlap Length (-L): Default is 40 bp. For high-fidelity HiFi datasets, increasing to 60-80 bp may reduce spurious alignments.

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graphBuild

graphBuild is used for manual seed selection, extension, and assembly graph reconstruction when autoMito requires fine-tuning.

Usage: PMAT graphBuild [-i SUBSAMPLE] [-a ASSEMBLY] [-o OUTPUT] [options]
Example:
       PMAT graphBuild -i assembly_out/subsample -a assembly_out/assembly_result -o graphBuild_result -s 1 312 356 -T 8
       PMAT graphBuild -i assembly_out/subsample -a assembly_out/assembly_result -o graphBuild_result -d 5 -s 1 312 356 -T 8

Required options:
   -i, --subsample     Input subsample directory (from autoMito)
   -a, --graphinfo     Input assembly result directory (from autoMito)
   -o, --output        Output directory

Optional options:
   -G, --organelles    Genome organelles (mt: mitochondria / pt: plastid, default: mt)
   -x, --taxo          Specify the organism type (0/1/2), 0: plants, 1: animals, 2: Fungi (default: 0)
   -d, --depth         Contig depth threshold for filtering
   -s, --seeds         Contig IDs for extending (separated by space, e.g., -s 1 312 356)
   -T, --cpu           Number of threads (default: 8)
   -h, --help          Show this help message and exit