Hercules: a profile HMM-based hybrid error correction algorithm for long reads.

ABSTRACT: Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several types of studies require long and accurate reads. In such cases researchers often combine both technologies and the erroneous long reads are corrected using the short reads. Current approaches rely on various graph or alignment based techniques and do not take the error profile of the underlying technology into account. Efficient machine learning algorithms that address these shortcomings have the potential to achieve more accurate integration of these two technologies. We propose Hercules, the first machine learning-based long read error correction algorithm. Hercules models every long read as a profile Hidden Markov Model with respect to the underlying

SUBMITTER: Firtina C 

PROVIDER: S-EPMC6265270 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature