Quick Start

Quick Start Guide

This guide describes standard assembly workflows for organellar genomes using PMAT2.

1. PacBio HiFi Data Assembly

HiFi reads offer high single-molecule accuracy. Assembly can be performed directly without pre-correction:

PMAT autoMito -i hifi.fastq.gz -o hifi_assembly -t hifi -m -T 8

Key options:

• -t hifi: Specifies PacBio HiFi sequencing mode.
• -m: Keeps sequence data in memory to reduce disk I/O and speed up computation.
• -T 8: Allocates 8 CPU threads.

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2. Oxford Nanopore (ONT) Data Assembly

ONT reads require error correction before assembly. You can specify NextDenovo or Canu:

# Using NextDenovo for error correction
PMAT autoMito -i ont.fastq.gz -o ont_assembly -t ont -S nextdenovo -N /path/to/nextDenovo -m -T 8

# Using Canu for error correction
PMAT autoMito -i ont.fastq.gz -o ont_assembly -t ont -S canu -C /path/to/canu -m -T 8

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3. PacBio CLR Data Assembly

Continuous Long Reads (CLR) also require error correction:

PMAT autoMito -i clr.fastq.gz -o clr_assembly -t clr -S canu -C /path/to/canu -m -T 8

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4. Selecting Organellar Target (-G) and Organism Taxonomy (-x)

By default, PMAT2 targets plant mitochondrial genomes (-G mt -x 0). You can adjust target organelles and taxonomy:

• -G mt: Assemble mitochondrial genome (default).
• -G pt: Assemble chloroplast (plastid) genome.
• -G all: Assemble both mitochondrial and chloroplast genomes.
• -x 0: Plants (default).
• -x 1: Animals.
• -x 2: Fungi.

Example (Animal Mitochondria):

PMAT autoMito -i animal_hifi.fq.gz -o animal_mt -t hifi -G mt -x 1 -m -T 8