PRICE

PRICE assembles and iteratively extends contigs using paired-read information to reconstruct genes, transcripts, and viral genomes from complex metagenomic datasets.

Key Features:

• Paired-Read Information Utilization: Leverages paired-read information to iteratively increase the size of existing contigs.
• Iterative Contig Extension: Implements an iterative extension strategy to grow contigs from seed sequences within complex datasets.
• Focused Assembly Strategy: Targets assembly to particular nucleic acid species within multicomponent metagenomic datasets to improve specificity.
• Supported Sequence Types: Applies to assembly of genes, transcripts, and virus genomes from metagenomic sequencing data.
• Demonstrated Performance: Has been used to assemble the BCBL-1 strain of Kaposi's sarcoma-associated herpesvirus from a metagenomic dataset.

Scientific Applications:

• Metagenomics and microbiome studies: Recovery of targeted sequences and contigs from complex microbial communities.
• Virology: Reconstruction of viral genomes from mixed-sample metagenomic data.
• Environmental genomics: Assembly of specific genetic elements from multicomponent environmental sequencing datasets.
• Targeted gene and transcript recovery: Identification and assembly of specific genes and transcripts within complex samples.

Methodology:

Leverages paired-read information and an iterative contig extension algorithm to focus assembly on particular nucleic acid species within multicomponent metagenomic datasets.