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Welcome to PMAT2 Documentation

PMAT2 is an efficient, specialized toolkit for the de novo assembly of mitochondrial and chloroplast genomes from PacBio HiFi, Oxford Nanopore (ONT), and PacBio CLR sequencing reads.

Key Features in Version 2.2.0

• Native Binary Execution: Bundled 64-bit core assembly engine under bin/, eliminating mandatory Apptainer / Singularity container dependencies for native execution.
• Universal Linux Compatibility: Statically compiled binary supporting all major Linux distributions (CentOS 7+, Rocky Linux, Ubuntu 18.04+, Debian 10+).
• All-in-One Standalone Container: Standalone .sif image provided on GitHub Releases for fully isolated execution with pre-configured NCBI BLAST+.
• Comprehensive Quality Assessment: Built-in orgAss module for automated completeness evaluation against conserved protein-coding gene databases.

Documentation Sitemap

• Installation: Step-by-step setup guides for precompiled archives, git clone, and SIF container.
• Quick Start: Basic usage commands for HiFi, ONT, and CLR sequencing data.
• Command Reference: Exhaustive documentation of command-line arguments for autoMito and graphBuild.
• Tutorials and Demos: Walkthroughs with real datasets (Arabidopsis thaliana, Malus domestica, Phaseolus vulgaris, Populus deltoides).
• Output Files: Detailed structure of assembly contigs, GFA graphs, FASTA results, and evaluation summaries.
• Troubleshooting and FAQ: Frequently asked questions, container storage mounts, and tips for complex graph unlooping.

Citation

If you use PMAT2 in your research, please cite:

• Fuchuan Han, Changwei Bi, Yicun Chen, Xiaogang Dai, Zefu Wang, Huaitong Wu, Ning Sun, et al. 2025. PMAT2: An Efficient Graphical Assembly Toolkit for Comprehensive Organellar Genomes. iMeta 4: e70064. https://doi.org/10.1002/imt2.70064
• Bi C, Shen F, Han F, Qu Y, et al. 2024. PMAT: an efficient plant mitogenome assembly toolkit using ultra-low coverage HiFi sequencing data. Horticulture Research. uhae023, https://doi.org/10.1093/hr/uhae023