VCFShark: how to squeeze a VCF file

Summary Variant Call Format (VCF) files with results of sequencing projects take a lot of space. We propose the VCFShark, which is able to compress VCF files up to an order of magnitude better than the de facto standards (gzipped VCF and BCF). The advantage over competitors is the greatest when compressing VCF files containing large amounts of genotype data. The processing speeds up to 100 MB/s and main memory requirements lower than 30 GB allow to use our tool at typical workstations even for large datasets. Availability and implementation https://github.com/refresh-bio/vcfshark. Supplementary information Supplementary data are available at Bioinformatics online.

VCFShark: how to squeeze a VCF file

SummaryThe VCF files with results of sequencing projects take a lot of space. We propose VCFShark squeezing them up to an order of magnitude better than the de facto standards (gzipped VCF and BCF).Availability and Implementationhttps://github.com/refresh-bio/[email protected] informationSupplementary data are available at publisher’s Web site.

Twentieth-Century Length: The Origins, Use, and Formalization of Electromagnetic Standards

There was a fundamental change in our standards of length during the twentieth century, as the metal bars that had served for so long gave way to standards based on the wavelength, and then velocity, of light. This article describes those changes with particular emphasis on the standards-in-use of practitioners at the frontier of precision: spectroscopists, industrialists, geodesists, and astronomers. It reveals a multiplicity of de facto standards that supported their various innovations in practical electromagnetic measurement techniques. These de facto standards often came before, and guided the adoption of, the more visible new de jure standards that have been the subject of greater historical attention. I also offer a new explanation of the processes of change in our standards of length, based not simply on the search for better precision but more on concepts of mutual grounding and coherence.