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We present Genozip, a universal and fully featured compression software for genomic data. Genozip is designed to be a general-purpose software and a development framework for genomic compression by providing five core capabilities-universality (support for all common genomic file formats), high compression ratios, speed, feature-richness and extensibility. Genozip delivers high-performance compression for widelyused genomic data formats in genomics research, namely FASTQ, SAM/BAM/CRAM, VCF, GVF, FASTA, PHYLIP and 23andMe formats. Our test results show that Genozip is fast and achieves greatly improved compression ratios, even when the files are already compressed. Further, Genozip is architected with a separation of the Genozip Framework from file-format-specific Segmenters and data-type-specific Codecs. With this, we intend for Genozip to be a general-purpose compression platform where researchers can implement compression for additional file formats, as well as new codecs for data types or fields within files, in the future. We anticipate that this will ultimately increase the visibility and adoption of these algorithms by the user community, thereby accelerating further innovation in this space., Availability and Implementation: Genozip is written in C. The code is open-source and available on http://www.genozip.com. The package is free for non-commercial use. It is distributed through the Conda package manager, github, and as a Docker container on DockerHub. Genozip is tested on Linux, Mac and Windows., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2021. Published by Oxford University Press.)

Motivation: genozip is a new lossless compression tool for Variant Call Format (VCF) files. By applying field-specific algorithms and fully utilizing the available computational hardware, genozip achieves the highest compression ratios amongst existing lossless compression tools known to the authors, at speeds comparable with the fastest multi-threaded compressors., Availability and Implementation: genozip is freely available to non-commercial users. It can be installed via conda-forge, Docker Hub, or downloaded from github.com/divonlan/genozip., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2020. Published by Oxford University Press.)

Summary: Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services., Availability and Implementation: Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu., Contact: dpwall@stanford.edu or peter_tonellato@hms.harvard.edu., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author 2014. Published by Oxford University Press.)