Kang Dongwan D, Li Feng, Kirton Edward, Thomas Ashleigh, Egan Rob, An Hong, Wang Zhong
Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.
School of Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui, China.
PeerJ. 2019 Jul 26;7:e7359. doi: 10.7717/peerj.7359. eCollection 2019.
We previously reported on MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent analyses of uncultivated microbial species. MetaBAT has become one of the most popular binning tools largely due to its computational efficiency and ease of use, especially in binning experiments with a large number of samples and a large assembly. MetaBAT requires users to choose parameters to fine-tune its sensitivity and specificity. If those parameters are not chosen properly, binning accuracy can suffer, especially on assemblies of poor quality. Here, we developed MetaBAT 2 to overcome this problem. MetaBAT 2 uses a new adaptive binning algorithm to eliminate manual parameter tuning. We also performed extensive software engineering optimization to increase both computational and memory efficiency. Comparing MetaBAT 2 to alternative software tools on over 100 real world metagenome assemblies shows superior accuracy and computing speed. Binning a typical metagenome assembly takes only a few minutes on a single commodity workstation. We therefore recommend the community adopts MetaBAT 2 for their metagenome binning experiments. MetaBAT 2 is open source software and available at https://bitbucket.org/berkeleylab/metabat.
我们之前报道过MetaBAT，这是一款自动化的宏基因组分箱软件工具，用于从微生物群落中重建单个基因组，以便随后对未培养的微生物物种进行分析。MetaBAT之所以成为最受欢迎的分箱工具之一，很大程度上是因为其计算效率高且易于使用，特别是在处理大量样本和大型组装的分箱实验中。MetaBAT要求用户选择参数来微调其灵敏度和特异性。如果这些参数选择不当，分箱准确性可能会受到影响，尤其是在质量较差的组装上。在此，我们开发了MetaBAT 2来克服这个问题。MetaBAT 2使用一种新的自适应分箱算法来消除手动参数调整。我们还进行了广泛的软件工程优化，以提高计算和内存效率。在100多个真实世界的宏基因组组装上，将MetaBAT 2与其他软件工具进行比较，结果显示其具有更高的准确性和计算速度。在单个普通工作站上，对一个典型的宏基因组组装进行分箱只需几分钟。因此，我们建议社区在宏基因组分箱实验中采用MetaBAT 2。MetaBAT 2是开源软件，可在https://bitbucket.org/berkeleylab/metabat获取。
