Plass

Plass assembles protein sequences de novo by translating sequencing reads to reconstruct proteins from complex metagenomic and metatranscriptomic datasets.

Key Features:

• High sensitivity and precision: Demonstrates recovery of approximately 2-10 times more protein sequences compared to existing methods.
• Six-frame translation: Translates sequencing reads into protein sequences across all six reading frames to consider all possible coding frames.
• Large-dataset scalability: Scales to very large datasets, demonstrated by assembly of a soil reference protein catalog with 2 billion sequences from 640 soil samples and a marine eukaryotic catalog with 292 million sequences from 775 marine eukaryotic metatranscriptomes.
• Algorithmic optimization: Uses an assembly algorithm optimized for sensitivity and precision to maximize sequence recovery from complex samples.

Scientific Applications:

• Metagenomics and metatranscriptomics assembly: Reconstruction of protein sequences from environmental sequencing reads to generate assemblies for downstream analysis.
• Reference catalog generation: Creation of large-scale protein reference catalogs for soil and marine eukaryotic environments.
• Protein discovery and characterization: Identification and characterization of novel proteins from environmental samples to inform studies of microbial diversity, function, ecology, evolution, and biotechnology.

Methodology:

Translates sequencing reads in six reading frames and performs de novo protein-level assembly using an algorithm optimized for sensitivity and precision.