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 or ARKS. Fill gaps in LINKS-derived scaffolds using Sealer or cobbler (

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 and the BioRxiv manuscript.

Current Release

GitHub release page for LINKS

All Releases

Version  Released  Description  Licenses  Status 
1.8.6 Mar 13, 2018 Use v1.8.5 if running LINKS to scaffold with long reads*. When pipelined with ARCS, LINKS v1.8.6 prioritizes paths with shorter gaps only when there are no ambiguous gap distance estimates with neighboring sequences GPLv3 final
1.8.5 Feb 01, 2017 Enhanced graph output when pipelined with ARCS GPLv3 final
1.8.4 Sep 14, 2016 License changed to GPLv3 GPLv3 final
1.8.3 Aug 08, 2016 v1.8.3 fixes a bug introduced in v1.8.1 that caused sequence overuse GPL final
1.8 Apr 18, 2016 Native support for iterative k-mer pair extraction at distinct length intervals GPL final
1.7 Mar 18, 2016 Support for scaffolding with MPET (jumping library) reads 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) GPL final
1.5.2 Sep 18, 2015 LINKS outputs a scaffold graph in gv format, with highlighted linkages and edge attributes GPL final
1.5.1 Jul 12, 2015 Bug fix GPL final
1.5 Apr 24, 2015 Bloom filter implementation for reduced memory usage and faster execution. GPL final
1.3 Apr 22, 2015 Added support for multiple input files and FASTQ files BCCA (academic use) final
1.2 Apr 12, 2015 Bug fix 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 BCCA (academic use) final
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