ABruijn: Difference between revisions
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==System Variables== | ==System Variables== | ||
* HPC_{{ | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
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If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
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) | |||
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Latest revision as of 20:09, 24 August 2022
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.
Required Modules
Parallel (OpenMP)
- gcc/5.2.0
- abruijn
System Variables
- HPC_ABRUIJN_DIR - installation directory
Citation
If you publish research that uses abruijn you have to cite it as follows:
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)