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. 2018 Aug 22;19(1):303.
doi: 10.1186/s12859-018-2315-y.

bioSyntax: syntax highlighting for computational biology

Artem Babaian  1   2 , Anicet Ebou  3 , Alyssa Fegen  4 , Ho Yin Kam  5 , German E Novakovsky  6 , Jasper Wong  7 , Dylan Aïssi  8 , Li Yao  9
Affiliations

bioSyntax: syntax highlighting for computational biology

Artem Babaian et al. BMC Bioinformatics. .

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: Command line interface; FASTA; FASTQ; SAM; Sublime; Syntax highlighting; VCF; Vim.

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The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
Syntax highlighting for sequence alignment map (.sam) file format. a Terminal screenshot of the ‘less HG00128_hgr1.sam’ command run i. normally or ii. with bioSyntax. Related information in the header and data sections are grouped by colours (genomic coordinates, green; sample information, pale blue ...) to improve legibility. Each data-row is an individual sequencing read. Iii. CIGAR alignment strings in particular can be highlighted such that they become substantially easier to read. b A broad view of the nucleotide and PHRED-score for 30 reads i. before, and ii. after syntax highlighting. Underlying information of about the data becomes intuitively visible such as PCR-duplicates (black arrow) and poor quality areas and reads (blue arrow) based on iii. PHRED score
Fig. 2
Fig. 2
bioSyntax nucleotide colour scheme. a The four primary bases are coloured in two pairs of contrasting colours. IUPAC ambiguous bases are then coloured in increasingly lighter tones of the approximately mixed colours. To accomodate 4-dimensional bases in 3-dimensional colours, aMino (A or C) and Keto (G or T) bases are darker. b A comparison of nucleotide colour-schemes in the literature. c bioSyntax colouring allows for approximation of a sequences GC-content by how warm (high GC) or cool (high AT) it appears
See this image and copyright information in PMC

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