|Title||poreTally: run and publish de novo nanopore assembler benchmarks|
|Author(s)||Lannoy, Carlos de; Risse, J.E.; Ridder, D. de|
|Source||Bioinformatics 35 (2019)15. - ISSN 1367-4803 - p. 2663 - 2664.|
|Publication type||Refereed Article in a scientific journal|
|Abstract||Summary: Nanopore sequencing is a novel development in nucleic acid analysis. As such, nanopore-sequencing hardware and software are updated frequently and extensively, which quickly renders peer-reviewed publications on analysis pipeline benchmarking efforts outdated. To provide the user community with a faster, more flexible alternative to peer-reviewed benchmark papers for
de novo assembly tool performance we constructed poreTally, a comprehensive
benchmarking tool. poreTally automatically assembles a given read set using several often-used assembly pipelines, analyzes the resulting assemblies for correctness and continuity, and finally generates a quality report, which can immediately be published on Github/Gitlab.
Availability and implementation: poreTally is available on Github at https://github.com/cvdelannoy/poreTally, under an MIT license.