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 (https://github.com/bcgsc/rails/).
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 and the BioRxiv manuscript.
Current Release
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 |