LINKS

Long Interval Nucleotide K-mer Scaffolder

Project Description

LINKS

LINKS is a genomics application for scaffolding or re-scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It provides a generic framework for scaffolding and can work on any sequences. Fill gaps in LINKS-derived scaffolds using Sealer (http://www.bcgsc.ca/platform/bioinfo/software/sealer).

About the author: www.renewarren.ca

LINKS performance on ONT data

(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.

Re-scaffolding the white spruce genome using LINKS utilizing information from another white spruce genotype assembly

(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 YangBenjamin P. VandervalkBahar BehsazAlbert 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.

Current Release
LINKS 1.8

Released Apr 18, 2016

Native support for iterative k-mer pair extraction at distinct length intervals
More about this release…

Download file Get LINKS for all platforms
links_v1-8.tar.gz

All Releases

Version Released Description Compatibility Licenses Status
1.8 Apr 18, 2016 Native support for iterative k-mer pair extraction at distinct length intervals More about this release… GPL final
1.7 Mar 18, 2016 Support for scaffolding with MPET (jumping library) reads More about this release… GPL final
1.6.1 Feb 24, 2016 Incorporation of the BC Genome Sciences Centre custom Bloom filter with the recursive nucleotide hash function (ntHash). More about this release… GPL final
1.5.2 Sep 18, 2015 LINKS outputs a scaffold graph in gv format, with highlighted linkages and edge attributes More about this release… GPL final
1.5.1 Jul 12, 2015 bug fix. More about this release… GPL final
1.5 Apr 24, 2015 Bloom filter implementation for reduced memory usage and faster execution. More about this release… GPL final
1.3 Apr 22, 2015 Added support for multiple input files and FASTQ files More about this release… BCCA (academic use) final
1.2 Apr 12, 2015 bug fix More about this release… BCCA (academic use) final
1.1 Jan 01, 2015 Included offset option (-o option), which enable LINKS to explore a wider k-mer space range when running iteratively Minor fixes: IUPAC codes are now preserved More about this release… BCCA (academic use) final
Project Resources

Project owner: Rene Warren