LRBinner

Description

LRBinner is a long-read binning tool that overcomes several limitations of our previous work MetaBCC-LR (ISMB 2020). The tool uses variational auto-encoders to bin error-prone long reads using coverage and composition.

Environment Modules

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

System Variables

HPC_LRBINNER_DIR - installation directory
HPC_LRBINNER_BIN - executable directory

Job Script Examples

See the LRBinner_Job_Scripts page for LRBinner Job script examples.

Citation

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

 @InProceedings{wickramarachchi_et_al:LIPIcs.WABI.2021.11,
   author =	{Wickramarachchi, Anuradha and Lin, Yu},
   title =	{{LRBinner: Binning Long Reads in Metagenomics Datasets}},
   booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
   pages =	{11:1--11:18},
   series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
   ISBN =	{978-3-95977-200-6},
   ISSN =	{1868-8969},
   year =	{2021},
   volume =	{201},
   editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
   publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
   address =	{Dagstuhl, Germany},
   URL =		{https://drops.dagstuhl.de/opus/volltexte/2021/14364},
   URN =		{urn:nbn:de:0030-drops-143644},
   doi =		{10.4230/LIPIcs.WABI.2021.11},
   annote =	{Keywords: Metagenomics binning, long reads, machine learning, clustering}
 }