LINKS
Long Interval Nucleotide K-mer Scaffolder
LINKS v2.0.0 René L. Warren, Yaman Malkoc, T. Murathan Goktas 2014-2022
email: rwarren [at] bcgsc [dot] ca
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.
Location and version:
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$ which LINKS
/local/cluster/links/bin/LINKS
$ LINKS --version
/local/cluster/links/bin/LINKS: illegal option -- -
Usage: LINKS v2.0.0
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help message:
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$ LINKS
Usage: LINKS v2.0.0
-f sequences to scaffold (Multi-FASTA format, required)
-s file-of-filenames, full path to long sequence reads or MPET pairs [see below] (Multi-FASTA/fastq format, required)
-m MPET reads (default -m 1 = yes, default = no, optional)
DO NOT SET IF NOT USING MPET. WHEN SET, LINKS WILL EXPECT A SPECIAL FORMAT UNDER -s
Paired MPET reads in their original outward orientation <- -> must be separated by :
>template_name ACGACACTATGCATAAGCAGACGAGCAGCGACGCAGCACG:ATATATAGCGCACGACGCAGCACAGCAGCAGACGAC
-d distance between k-mer pairs (ie. target distances to re-scaffold on. default -d 4000, optional)
Multiple distances are separated by comma. eg. -d 500,1000,2000,3000
-k k-mer value (default -k 15, optional)
-t step of sliding window when extracting k-mer pairs from long reads (default -t 2, optional)
Multiple steps are separated by comma. eg. -t 10,5
-j threads (default -j 3, optional)
-o offset position for extracting k-mer pairs (default -o 0, optional)
-e error (%) allowed on -d distance e.g. -e 0.1 == distance +/- 10% (default -e 0.1, optional)
-l minimum number of links (k-mer pairs) to compute scaffold (default -l 5, optional)
-a maximum link ratio between two best contig pairs (default -a 0.3, optional)
*higher values lead to least accurate scaffolding*
-z minimum contig length to consider for scaffolding (default -z 500, optional)
-b base name for your output files (optional)
-r Bloom filter input file for sequences supplied in -s (optional, if none provided will output to .bloom)
NOTE: BLOOM FILTER MUST BE DERIVED FROM THE SAME FILE SUPPLIED IN -f WITH SAME -k VALUE
IF YOU DO NOT SUPPLY A BLOOM FILTER, ONE WILL BE CREATED (.bloom)
-p Bloom filter false positive rate (default -p 0.001, optional; increase to prevent memory allocation errors)
-x Turn off Bloom filter functionality (-x 1 = yes, default = no, optional)
-v Runs in verbose mode (-v 1 = yes, default = no, optional)
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software ref: https://github.com/bcgsc/LINKS
research ref: https://doi.org/10.1186/s13742-015-0076-3