CDKAM: a taxonomic classification tool using discriminative k-mers and approximate matching strategies.

ABSTRACT:

Background

Current taxonomic classification tools use exact string matching algorithms that are effective to tackle the data from the next generation sequencing technology. However, the unique error patterns in the third generation sequencing (TGS) technologies could reduce the accuracy of these programs.

Results

We developed a Classification tool using Discriminative K-mers and Approximate Matching algorithm (CDKAM). This approximate matching method was used for searching k-mers, which included two phases, a quick mapping phase and a dynamic programming phase. Simulated datasets as well as real TGS datasets have been tested to compare the performance of CDKAM with existing methods. We showed that CDKAM performed better in many aspects, especially when classifying TGS data w

SUBMITTER: Bui VK 

PROVIDER: S-EPMC7576720 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature