In modern genomics, mapping reads to a single reference genome is common practice. However, a reference genome does not necessarily accurately represent a population or species and as a result a substantial percentage of reads often cannot be mapped. A number of graph-based variation-aware mapping methods have recently been proposed to remedy this. Here, we propose an alternative multi-reference approach, which aligns reads to large collections of genomes simultaneously. Our approach, an extension to our pangenomics suite PanTools (https://git.wur.nl/bioinformatics/pantools), is as accurate as state-of the-art tools but more efficient on large numbers of genomes. We successfully applied PanTools to map genomic and metagenomic reads to large collections of viral, archaeal, bacterial, fungal and plant genomes.
- Downloaded 512 times
- Download rankings, all-time:
- Site-wide: 36,602 out of 103,809
- In bioinformatics: 4,591 out of 9,474
- Year to date:
- Site-wide: 28,195 out of 103,809
- Since beginning of last month:
- Site-wide: 33,244 out of 103,809
Downloads over time
Distribution of downloads per paper, site-wide
- 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!