Version: 2.2b
ABruijn is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. The package includes a polisher module, which produces assembly of high nucleotide-level quality.
Since the version 2.0, ABruijn performs additional repeat analysis step, which improves the structural accuracy of the resulting sequence. The algorithm also produces a graph representation of the final assembly.
ABruijn has moderate memory requirements and is designed to run on a single node. Typically, assembly of a bacteria with 50x coverage takes less than half an hour on a modern desktop and yeast assembly takes about 2 hours. A metagenome of total size 200 Mbp can be assembled within a day on using 70Gb of memory and 20 CPUs.
See the docs/INSTALL.md file.
See the docs/USAGE.md file.
Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W Shen, Mark Chaisson and Pavel Pevzner, "Assembly of Long Error-Prone Reads Using de Bruijn Graphs", PNAS 2016
ABruijn package includes some third-party software:
- libcuckoo [http://github.com/efficient/libcuckoo]
- intervaltree [https://github.com/ekg/intervaltree]
- lemon [http://lemon.cs.elte.hu/trac/lemon]
- BLASR [https://github.com/PacificBiosciences/blasr]
ABruijn is distributed under a BSD license. See the 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 fenderglass@gmail.com