Gonomics: Uniting high performance and readability for genomics with Go.
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2023-08
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Abstract
Many existing software libraries for genomics require researchers to pick between competing considerations: the performance of compiled languages and the accessibility of interpreted languages. Go, a modern compiled language, provides an opportunity to address this conflict. We introduce Gonomics, an open-source collection of command line programs and bioinformatic libraries implemented in Go that unites readability and performance for genomic analyses. Gonomics contains packages to read, write, and manipulate a wide array of file formats (e.g. FASTA, FASTQ, BED, BEDPE, SAM, BAM, and VCF), and can convert and interface between these formats. Furthermore, our modular library structure provides a flexible platform for researchers developing their own software tools to address specific questions. These commands can be combined and incorporated into complex pipelines to meet the growing need for high-performance bioinformatic resources. Gonomics is implemented in the Go programming language. Source code, installation instructions, and documentation are freely available at https://github.com/vertgenlab/gonomics.
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Au, Eric H, Christiana Fauci, Yanting Luo, Riley J Mangan, Daniel A Snellings, Chelsea R Shoben, Seth Weaver, Shae K Simpson, et al. (2023). Gonomics: Uniting high performance and readability for genomics with Go. Bioinformatics (Oxford, England). p. btad516. 10.1093/bioinformatics/btad516 Retrieved from https://hdl.handle.net/10161/28963.
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Craig Lowe
Craig Lowe is an Assistant Professor in the Department of Molecular Genetics and Microbiology. His research interests are in understanding how traits and characteristics of humans, and other vertebrates, are encoded in their genomes. He is especially focused on adaptations and disease susceptibilities that are unique to humans. To address these questions, Craig uses both computational and experimental approaches. Craig's recent research has been on differences in how genes are regulated between species, or between different individuals within a species, and how this causes traits to differ. All students in Craig's lab are exposed to an interdisciplinary environment; current lab members have backgrounds in mathematics, computer science, neuroscience, developmental biology, and genetics. Each year Craig teaches one or two courses on rotating topics of: ancient DNA, ethical issues in genomics, and software development for genetic analyses.
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