The BESST scaffolder

Created by Kristoffer Sahlin, the BESST scaffolder builds on an unbiased model for estimating the distance between two contigs using information about the paired-end or mate-pair library used for scaffolding.

Availability

BESST is written in Python and is available on Kristoffer's GitHub repository. See the file docs/INSTALL.md for access instructions. The easiest way to install BESST is, however, probably to use pip or easy_install:

  sudo pip install BESST

Or:

  sudo easy_install BESST

References

Please cite the following manuscripts!

• Sahlin, Street, Lundeberg, Arvestad; Improved gap size estimation for scaffolding algorithms; Bioinformatics, 2012.
• Sahlin, Vezzi, Nystedt, Lundeberg, Arvestad; BESST-efficient scaffolding of large fragmented assemblies; BMC Bioinformatics, 2014.
• Sahlin, Chikhi, Arvestad; Assembly scaffolding with PE-contaminated mate-pair libraries; Bioinformatics, 2016.