Description

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). It is also used to scaffold contig pairs linked by ARCS/ARKS. This module is for LINKS >=2.0.0 and does not support MPET input.

Input

Name
Description
Pattern

0 ()

1 ()

0 ()

1 ()

Output

Name
Description
Pattern

log ()

pairing_distribution ()

pairing_issues ()

scaffolds_csv ()

scaffolds_fasta ()

bloom ()

scaffolds_graph ()

assembly_correspondence ()

simplepair_checkpoint ()

tigpair_checkpoint ()

versions ()

Tools

links Documentation

Long Interval Nucleotide K-mer Scaffolder

doi: 10.1186/s13742-015-0076-3License: GPL v3
Authors