Novoalign

Novoalign is a sequencing tool that indexes the reference genome and is one of the nine mapping tools that were extensively analyzed and compared in a benchmarking suite that evaluated the different factors affecting the mapping process. The development of next-generation sequencing instruments has led to the generation of millions of short sequences in a single run. Aligning these reads to a reference genome is time-consuming and demands the development of fast and accurate alignment tools. However, the currently proposed tools make different compromises between the accuracy and the mapping speed. Many important aspects are overlooked while comparing the performance of a newly developed tool to the state of the art. Therefore, there is a need for an objective evaluation method that covers all the aspects.

In the benchmarking tests, Novoalign was compared with eight well-known mapping tools: Bowtie, Bowtie2, BWA, SOAP2, MAQ, RMAP, GSNAP, and mrsFAST (mrFAST), using synthetic data and real RNA-Seq data. MAQ and RMAP are based on building hash tables for the reads, whereas the remaining tools are based on indexing the reference genome. The benchmarking tests reveal the strengths and weaknesses of each tool, and the results show that no single tool outperforms all others in all metrics. However, Bowtie maintained the best throughput for most of the tests, while BWA performed better for longer read lengths.

The authors’ benchmarking tests reveal that Novoalign performs well in accuracy but is slower than other tools tested, such as Bowtie and BWA. Therefore, the choice of tool should depend on the user's specific needs. The mapping process is still a hard problem that is affected by many factors, and the benchmarking suite objectively compared the different factors affecting the mapping process. However, no tool outperforms all of the others in all the tests, and the end user should specify his needs to choose the tool that provides the best results.