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Fig. 1 | BMC Bioinformatics

Fig. 1

From: bioSyntax: syntax highlighting for computational biology

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

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