poreTally: run and publish de novo nanopore assembler benchmarks

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frequently and extensively, which quickly renders peer-reviewed publications on analysis pipeline benchmarking efforts outdated.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.

Supplementary information: Supplementary data are available at Bioinformatics online.