BLITSFR: scalable comparative genomics with self-contained interactive single file report

Abstract

Comparative genomics routinely requires the alignment of query genomes against a reference to delineate conserved and variable regions, yet existing tools often produce static visualisations or necessitate centralised web services and data uploads. To address this, we present BLITSFR (BLAST Interactive Tracks in Single-File Report), a command-line tool that compares query genomes against a reference and returns a single interactive HTML file. The report opens in any modern browser, requiring no server or data upload, and lets users explore conserved and variable regions across the genomes. BLITSFR handles both assembled genomes and raw reads, and processes hundreds of genomes in minutes on a standard laptop with genome tracks sorting, filtering, and colouring by metadata are performed within the report, without requirement for re-running the analysis. We demonstrate its utility by analysing vancomycin-resistant Enterococcus faecium ST78 genomes to confirm the conservation of Tn1549-like transposons and a case of β-lactam-resistant Corynebacterium diphtheriae, where coverage depth resolved resistance transposon copy number. BLITSFR and SCIFR are freely available at the provided GitHub repositories (https://github.com/nalarbp/blitsfr, https://github.com/nalarbp/scifr).