PRICE de novo (meta)genome assembler

PRICE (Paired-Read Iterative Contig Extension) is a command-line de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, those contigs can be individual reads from a subset of the paired-read dataset, non-paired reads from sequencing technologies that provide non-paired data, or contigs that were output from a prior run of PRICE or any other assembler.

PRICE was designed to address the challenge of assembling viral genomes that comprise a small minority of the reads within ultra-deep, short-read, shotgun metagenomic datasets. PRICE has already enabled the discovery of several novel virus genomes from such complex datasets, and it is also being applied to the de novo assembly of large individual genomes.