MetaPlatanus

MetaPlatanus assembles metagenomic short reads and long-range sequencing data (Oxford-Nanopore, PacBio, mate-pair libraries, 10x linked reads) to produce high-contiguity draft genomes and minimize inter-species misassemblies.

Key Features:

• Hybrid Assembly Approach: Constructs initial contigs from accurate short reads and iteratively incorporates long-range links from Oxford-Nanopore, PacBio, mate-pairs, and 10x linked reads (experimental) to extend contigs.
• Integration of Multiple Data Types: Integrates coverage depths, k-mer frequencies, and binning results to refine assemblies, correct misassemblies, and reduce inter-species misassemblies.
• Automated Multi-step Process: Automates contig assembly, scaffolding, gap closing, and binning.

Scientific Applications:

• Draft Genome Recovery: Recovers multiple draft genomes from metagenomic data, including genomes of uncultured organisms.
• Metagenome Structural Analysis: Produces high-contiguity assemblies suitable for exploring large-scale structures within metagenomes.
• Benchmarking and Element Recovery: Assembles coding genes, gene clusters, viral sequences, and substantial portions of bacterial genomes in mock datasets and human gut and saliva metagenomes.

Methodology:

Performs initial assembly from short-read paired-end libraries followed by iterative refinement using long-range information and species-specific sequence composition and coverage depth, and leverages binning information to assemble near-complete genomes, particularly for high-abundance bacterial species.