Raven

Raven assembles genomes de novo from long uncorrected reads produced by Pacific Biosciences and Oxford Nanopore Technologies, addressing the high error rates of third-generation sequencing.

Key Features:

• De novo assembly: Assembles genomes directly from long uncorrected reads without requiring a reference.
• Long-read support: Explicitly supports Pacific Biosciences and Oxford Nanopore Technologies long-read data characteristic of third-generation sequencing.
• Error handling: Employs algorithms to manage the inherent high error rates of long-read sequencing to produce high-quality assemblies without extensive preprocessing or error correction.
• Computational efficiency: Achieves high speed and low memory consumption across benchmarked datasets.
• Accuracy: Produces assembly accuracy comparable to other leading assemblers for third-generation sequencing datasets (DOI: 10.1101/2020.08.07.242461).

Scientific Applications:

• De novo genome assembly: Generating genome assemblies from Pacific Biosciences and Oxford Nanopore Technologies long-read datasets.
• Large-scale genomic projects: Assembly of large datasets where speed and memory efficiency are important considerations.
• Downstream analyses: Producing assemblies suitable for subsequent analyses and applications.

Methodology:

Raven applies algorithms that manage errors in long uncorrected long-read sequencing data to produce high-quality assemblies without extensive preprocessing or error correction.