ABruijn

Description

abruijn website

ABruijn is a de novo assembler for PacBio and Oxford Nanopore Technologies reads. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. First, the algorithm produces a draft assembly by concatenating different parts of raw reads. This coarse sequence is then polished into a high quality assembly.

ABruijn works for both bacterial and eukaryotic genomes. Typically, assembly of a bacteria with 50x coverage takes less than an hour on a modern desktop, while yeast assembly takes about 5 hours. A eukaryotic genome of size 200 Mbp can be assembled within a day on a computational server.

Environment Modules

Run module spider abruijn to find out what environment modules are available for this application.

Environment Variables

• HPC_ABRUIJN_DIR - installation directory
• HPC_ABRUIJN_BIN - executable directory

Citation

If you publish research that uses this software you have to cite it as follows:

Lin, Y., Yuan, J., Kolmogorov, M., Shen, M. W., & Pevzner, P. A. (2016). Assembly of long error-prone reads using de Bruijn graphs. bioRxiv, 048413. https://doi.org/10.1101/048413

Categories

biology, assembly, ngs