poreTally: run and publish de novo nanopore assembler benchmarks

Carlos de Lannoy; Judith Risse; Dick de Ridder

doi:10.1101/424184

poreTally: run and publish de novo nanopore assembler benchmarks

Carlos de Lannoy (Corresponding author), Judith Risse, Dick de Ridder

NIOO - Animal Ecology (AnE)

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Abstract

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frequently and extensively, which quickly renders peer-reviewed publications on analysis pipeline benchmarking efforts outdated.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.poreTally is available on Github at https://github.com/ cvdelannoy/poreTally, under an MIT license.Supplementary data are available at Bioinformatics online.

Original language	English
Pages (from-to)	2663-2664
Number of pages	2
Journal	Bioinformatics
Volume	35
Issue number	15
DOIs	https://doi.org/10.1101/424184 https://doi.org/10.1093/bioinformatics/bty1045
Publication status	Published - 2019

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national

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abstract = "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frequently and extensively, which quickly renders peer-reviewed publications on analysis pipeline benchmarking efforts outdated.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.poreTally is available on Github at https://github.com/ cvdelannoy/poreTally, under an MIT license.Supplementary data are available at Bioinformatics online.",

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AU - Risse, Judith

AU - de Ridder, Dick

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poreTally: run and publish de novo nanopore assembler benchmarks

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