Recent Releases of besst

An order of magnitude more efficient path traversal algorithm. It reduces the number of paths tried based on an DP (-ish) algorithm, therefore we can explore more of the graph in less time. This should give better quality scaffolds compared to older versions.
Betteer scoring of edges when library distribution is positively skwed (long tail) by fit to lognormal distribution.
Added better logging to Statistics.txt and fixed minor logging bugs.
Added an output file repeatslog.tsv on the following format: `contigaccession length coverage cov/meancov(exp number of placements) libmean placable`. This file serves as som information to future repeat placement in scaffolding.
Added parameters -z_min (lower coverage cutoff), -max_contig_overlap how many bases in contig ends that are merged between two adjacent contigs in a created scaffold (default 200).

- Python
Published by ksahlin almost 10 years ago

Ability to detect and scaffold with PE-contamination
More efficient (in practice) way to find paths with "good score" in contig graph.
Speed-ups in pathfinding algorithm
Better inference of gap sized when library is skewed (log-normal fitting - extending GapEst's assumptions of normal distribution)
Better inference of library insert size distribution on fragmented assemblies (based on theory from http://www.biorxiv.org/content/early/2015/08/04/023929.abstract)

- Python
Published by ksahlin over 10 years ago

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