bioSyntax: syntax highlighting for computational biology

Abstract

Abstract Background Computational biology requires the reading and comprehension of biological data files. Plain-text formats such as SAM, VCF, GTF, PDB and FASTA, often contain critical information which is obfuscated by the data structure complexity. Results bioSyntax (https://biosyntax.org/) is a freely available suite of biological syntax highlighting packages for vim, gedit, Sublime, VSCode, and less. bioSyntax improves the legibility of low-level biological data in the bioinformatics workspace. Conclusion bioSyntax supports computational scientists in parsing and comprehending their data efficiently and thus can accelerate research output.

Keywords

• Syntax highlighting
• Vim
• Sublime
• Command line interface
• SAM
• VCF