Version: 0.4b
ABruijn is a de novo assembler for Pacbio and Oxford Nanopore reads. The algorithm is based on A-Bruijn graph and bypasses initial error-correction step, producing a draft assembly of read-like quiality. This coarse sequence is then polished to a high quality assembly.
ABruijn works with both bacterial and eukaryotic genomes. Typically, assembly of a bacteria with 55x coverage takes less than an hour on a modern desktop, while yeast assembly takes about 5 hours. A eukariotyc genome of size 200 Mbp could be assembled within a day on a computational server with 64 CPUs.
See docs/INSTALL.md file.
See docs/USAGE.md file.
Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W Shen, Pavel Pevzner, "Assembly of Long Error-Prone Reads Using de Bruijn Graphs" (http://biorxiv.org/content/early/2016/04/13/048413)
ABruijn package includes some third-patry software:
- libcuckoo [http://github.com/efficient/libcuckoo]
ABruijn is dictributed under BSD license. See LICENSE file for details.
ABruijn was developed in Pavel Pevzner's lab at UCSD
Code contributions:
- Original assembler code: Yu Lin
- Original polisher code: Jeffrey Yuan
- Current package: Mikhail Kolmogorov
Please report any problems directly to the github issue tracker. Also, you can send feedback to [email protected]