Version 2.2.4

• 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 repeats_log.tsv on the following format: contig_accession length coverage cov/mean_cov(exp number of placements) lib_mean 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).

BESST-v2

• 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)