Summary: The assignment of Y chromosome data to related clusters, or haplogroups, is a common application in human population genetics. To enable this at scale, we developed SNAPPY. SNAPPY is a software program used to assign Y-chromosome phylogeny-informed haplotypes using dense genotype data. The program efficiently tests all haplotypes in a provided Y-chromosome database to find the haplogroup that is best supported by the input genotypes. Importantly, the method considers both the amount of support for the specific haplogroup, as well as its ancestral haplogroups via parsimony. This accounts for the underlying genealogy the haplotypes represent, strengthening the accuracy of the assignments. SNAPPY is fast, scalable, and uses standard file formats, making it easy to integrate into analytical pipelines. Availability and Implementation: The program is implemented in python. The program, a user manual, haplotype databases, and test datasets are available for download at github.com/chrisgene/snappy. Contact: Jonathan.email@example.com, Chris.firstname.lastname@example.org
- Downloaded 420 times
- Download rankings, all-time:
- Site-wide: 40,966 out of 94,912
- In bioinformatics: 4,955 out of 8,837
- Year to date:
- Site-wide: 35,169 out of 94,912
- Since beginning of last month:
- Site-wide: 68,170 out of 94,912
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!