Sealer

Scalable gap-filler for finishing large genomes

Project Description

While next-generation sequencing technologies have made sequencing genomes faster and more affordable, deciphering the complete genome sequence of an organism remains out of reach, especially for large genomes. At the moment, most finishing efforts are semi-automated procedures requiring painstaking manual efforts and specialized labor.

Sealer is a scalable tool designed to close gaps within assembly scaffolds. Sealer is a stand-alone application of Konnector, a fast and low-memory Bloom filter-based de bruijn graph assembler. It identifies problematic regions (those with Ns) in a user-input scaffold file, targets the gaps for assembly iteratively using a range of k values and consolidates assembled fragments into a new draft genome assembly.

Sealer scales to successfully close 35.6% and 13.8% of gaps in H. sapiens (3Gbp) and P. glauca assemblies in under 7 hours and 27 hours, respectively – a feat that is not possible with other tools. We expect Sealer to have broad utility for finishing genomes across the tree of life, from bacterial genomes to large plant genomes and beyond.

Availability

Sealer is included with ABySS 1.9.0. and later, and is available for download from http://www.bcgsc.ca/platform/bioinfo/software/abyss.

Citation

Paulino, Daniel, René L. Warren, Benjamin P. Vandervalk, Anthony Raymond, Shaun D. Jackman, and Inanç Birol. "Sealer: a scalable gap-closing application for finishing draft genomes." BMC Bioinformatics 16, no. 1 (2015): 230. http://www.biomedcentral.com/1471-2105/16/230