plasmidspades

plasmidspades assembles plasmid genomes using SPAdes (St. Petersburg genome assembler) to reconstruct plasmid sequences from single-cell and multicell sequencing data.

Key Features:

• SPAdes-based framework: Builds on the SPAdes (St. Petersburg genome assembler) framework for assembly.
• Single-cell and multicell assembly: Performs assembly for both single-cell and multicell sequencing datasets.
• Artifact handling: Addresses non-uniform read coverage, sequencing errors, and chimeric reads typical of single-cell data.
• Plasmid-focused assembly: Specifically targets reconstruction of plasmid genomes from sequence data.
• Improved performance: Demonstrates improved assembly performance compared to E+V-SC, Velvet, and SoapDeNovo for genomes of uncultivable bacteria.

Scientific Applications:

• Single-cell genomics: Enables assembly of whole-genome sequences from uncultivated organisms in single-cell studies.
• Metagenomic complement: Complements gene-centric metagenomic studies by enabling plasmid reconstruction.
• Microbial diversity and function: Facilitates recovery of plasmid sequences to support analyses of microbial diversity and function across environmental samples.

Methodology:

Based on the SPAdes assembler, it applies computational techniques to manage non-uniform read coverage, sequencing errors, and chimeric reads in single-cell and multicell assemblies.