If you are interested in the detailed methodology, please refer to our manuscript, bioSyntax: syntax highlighting for computational biology, for more information.
Summary
bioSyntax is a tool designed to simplify the inspection of biological sequences, regions, and alignments. It is compatible with multiple text editors such as vim, VS Code, sublime, less, and gedit.
It provides syntax highlighting for various file formats including FASTA, FASTQ, CWL, BED, GTF, PDB, PML, SAM, and VCF.
This tool is a collaboration between Artem Babaian (lead developer), Anicet Ebou, Alyssa Fegen, Ho Yin Kam, German E. Novakovsky, Jasper Wong, Dylan Aïssi, and me.
Availability
bioSyntax can be accessed through the accompany package control tools for most of the text editors. For example, if you are a Visual Studio Code user, you can install bioSyntax via Visual Studio Marketplace.
Demo
1 @HD VN:1.0 SO:coordinate 2 @SQ SN:chr13 LN:1023550 3 @RG ID:ERR194147 LB:NA12878_pp SM:NA12878 PL:ILLUMINA PU:HSQ1004 4 @PG ID:bowtie2 PN:bowtie2 VN:2.2.6 CL:"/usr/bin/bowtie2-align-s 5 ERR194147.58035754 137 chr13 10001 22 78S23M = 10001 0 6 ERR194147.58035757 73 chr13 10001 22 66S35M = 10001 0 7 ERR194147.58035758 137 chr13 10001 22 78S23M = 10001 0 8 ERR194147.58035764 73 chr13 10001 22 70S31M = 10001 0 9 ERR194147.58035769 137 chr13 10001 22 44S37M1D3M1I16M = 1000 10 ERR194147.58035774 73 chr13 10001 22 66S35M = 10001 0 11 ERR194147.58035775 73 chr13 10001 24 24S37M1D3M1I18M3I14M1S = 12 ERR194147.58035778 137 chr13 10001 22 38S59M4S = 1000 13 ERR194147.58035781 137 chr13 10001 22 73S28M = 10001 0 14 ERR194147.58035780 73 chr13 10001 22 54S47M = 10001 0 15 ERR194147.58035779 137 chr13 10001 28 5S37M1D3M1I18M5D29M8S = 16 ERR194147.58035785 73 chr13 10001 22 73S28M = 10001 0 17 ERR194147.58035788 73 chr13 10001 22 51S37M1D3M1I9M = 1000 18 ERR194147.58035784 137 chr13 10001 24 15S59M5D27M = 1000 19 ERR194147.58035789 73 chr13 10001 22 38S37M1D3M1I18M4S = 20 ERR194147.58035787 137 chr13 10001 28 11S37M1D3M1I18M5D30M1S = 21 ERR194147.58035792 73 chr13 10001 22 63S31M7S = 1000 22 ERR194147.58035790 73 chr13 10001 22 26S37M1D3M1I18M3I13M = 23 ERR194147.58035797 73 chr13 10001 22 33S37M1D3M1I18M9S = 24 ERR194147.58035978 73 chr13 10001 24 35S65M1S = 1000 25 ERR194147.58278197 163 chr13 10001 24 65S36M = 10009 174 26 ERR194147.58278237 163 chr13 10001 24 45S56M = 10200 355 27 ERR194147.58278235 163 chr13 10001 22 58S43M = 10187 355 28 ERR194147.58278245 163 chr13 10001 22 74S27M = 10258 429 29 ERR194147.58278246 163 chr13 10001 28 43S58M = 10258 401 30 ERR194147.58278244 99 chr13 10001 24 55S46M = 10258 411 31 ERR194147.58278243 99 chr13 10001 28 11S90M = 10247 358 32 ERR194147.58278250 99 chr13 10001 24 62S37M2S = 1025:
Source: asciinema