LINKS

Long Interval Nucleotide K-mer Scaffolder

Project Description

LINKS is a scalable genomics application for scaffolding or re-scaffolding genome assembly drafts with long reads, such as those produced by Oxford Nanopore Technologies Ltd and Pacific Biosciences. It provides a generic alignment-free framework for scaffolding and can work on any sequences. It is versatile and supports not only long sequences as a source of long-range information, but also MPET pairs and linked-reads, such as those from the 10x Genomics GemCode and Chromium platform, via ARCS (http://www.bcgsc.ca/platform/bioinfo/software/arcs) or ARKS (https://github.com/bcgsc/arks/). Fill gaps in LINKS-derived scaffolds using Sealer (http://www.bcgsc.ca/platform/bioinfo/software/sealer) or cobbler (https://github.com/bcgsc/rails/).

About the author: www.renewarren.ca

(top) LINKS performance for scaffolding high-quality Illumina assemblies using Oxford Nanopore Technologies long reads (F2D: Full 2 Dimension, R7 or R7.3 chemistry) compared to other scaffolders (SSPACE-LR, AHA) developed for Pacific Biosciences sequence data.

(top) LINKS-rescaffolded white spruce (PG29-V3, 20 Gbp) genome draft using the draft assembly of another colossal 20 Gbp white spruce genotype (WS77111-V1) draft genome assembly. The merges were validated by gap-filling and MPET read alignment.

Citing

If you use LINKS in your research, please cite:

René L. Warren^*, Chen Yang, Benjamin P. Vandervalk, Bahar Behsaz, Albert Lagman,Steven J. M. Jones and Inanç Birol. 2015. LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. GigaScience. 4:35

Additional information about LINKS is found in the readme file provided in the latest release, the BioRxiv manuscript and in this poster.