LINKS is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc).

Input:

LINKS does not use quality information in the Reads, so it is recommended to filter the long reads first.

Provide a fasta or fasta.gz dataset containing the Contigs, and a fastq, fastq.gz, fasta or fasta.gz dataset of Reads to be used for scaffolding.

Use cases:

• Use long reads to scaffold a draft assembly by providing the draft assembly to the Contigs parameter and the long reads to the Reads parameter.
• Use a reference assembly to scaffold a draft assembly by providing the reference assembly to the Reads parameter. For example, you could use a species’s reference genome to scaffold a genome that was assembled for another individual.

How it works:

LINKS uses k-mer pairs from the Reads to identify candidate pairs of Contigs, then uses the number of spanning k-mer pairs and the mean distance between them to build scaffolds.

You can control the distance between k-mer pairs, the length of the k-mers and the minimum number of k-mer pairs between contigs. See the LINKS readme on GitHub for information on setting advanced parameters.