LINKS 1.8 (Apr 18, 2016)


Native support for iterative k-mer pair extraction at distinct length intervals

For additional information about this project, please visit the overview page .

Available downloads


For all platforms (1.1 MB)

Release Notes

State Final release
License GPL
Release Manager Rene Warren

In v1.8, Users may input multiple distances using the -d parameter, separating each distance by a comma.
eg. -d 500,1000,2000,4000,5000
This will have for effect to extract kmer pairs at these five distance intervals.

Similarly, the window step size now accepts multiple integers, each separated by a comma and with the order matching that in -d. However, the size of the array can be shorter, and the last valid -t will be propagated to subsequent distances when they are not defined.
eg. -t 20,10,5
A step size of 20, 10, 5, 5, 5 bp will be used when exploring the distances supplied above.

In v1.8, a single round of scaffolding is done, using the kmer pair space extracted at the specified distances.
Accordingly, v1.8 is not expected to yield the exact same results as separate iterative LINKS runs. For users comfortable with the original set up, no change is needed to make use of the previous LINKS behavior.

Simultaneous exploration of vast kmer space is expected to yield better scaffolding results.

Specifying many distances will require large amount of RAM, especially with
low -t values.