Long Interval Nucleotide K-mer Scaffolder
LINKS is a 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 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 10X Genomics GemCode and Chromium data via ARCS (http://www.bcgsc.ca/platform/bioinfo/software/arcs). Fill gaps in LINKS-derived scaffolds using Sealer (http://www.bcgsc.ca/platform/bioinfo/software/sealer).
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.
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
Released Sep 14, 2016
license changed to GPLv3
More about this release…
- Get LINKS for all platforms
|1.8.4||Sep 14, 2016||license changed to GPLv3 More about this release…||GPLv3||final|
|1.8.3||Aug 08, 2016||v1.8.3 fixes a bug introduced in v1.8.1 that caused sequence overuse More about this release…||GPL||final|
|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|