Nanopore sequencing is a novel approach to nucleic acid analysis that generates long, error-prone reads. Since device components, base calling software and best practices for sample preparation are updated frequently and extensively, the nature of the produced data also changes frequently. As a result, peer-reviewed publications on de novo assembly pipeline benchmarking efforts are quickly rendered outdated by the next major improvement to the sequencing platforms. 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. Results can immediately be shared with peers in a Github/Gitlab repository. Furthermore, we aim to give a more inclusive overview of assembly pipeline performance than any individual research group can, by offering users the possibility to submit their results to a collective benchmarking effort. poreTally is available Github: https://github.com/cvdelannoy/poreTally .
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- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!