S-conLSH: alignment-free gapped mapping of noisy long reads.

ABSTRACT:

Background

The advancement of SMRT technology has unfolded new opportunities of genome analysis with its longer read length and low GC bias. Alignment of the reads to their appropriate positions in the respective reference genome is the first but costliest step of any analysis pipeline based on SMRT sequencing. However, the state-of-the-art aligners often fail to identify distant homologies due to lack of conserved regions, caused by frequent genetic duplication and recombination. Therefore, we developed a novel alignment-free method of sequence mapping that is fast and accurate.

Results

We present a new mapper called S-conLSH that uses Spaced context based Locality Sensitive Hashing. With multiple spaced patterns, S-conLSH facilitates a gapped mapping of noisy long reads to

SUBMITTER: Chakraborty A 

PROVIDER: S-EPMC7879691 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature