ABruijn¶
Description¶
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:
Categories¶
biology, assembly, ngs