BIGSdb dependencies

Required packages

BIGSdb requires a number of software components to be installed:

Linux packages

  • Apache2 web server with mod_perl2

  • PostgreSQL database 9.5+

  • Perl 5.22+

  • BioPerl

  • BLAST+


    • infoalign - use to extract alignment stats in Genome Comparator.

    • sixpack - used to translate sequences in multiple reading frames.

    • stretcher - used for sequence alignment in allele query.

  • Ipcress - part of exonerate package - used to simulate PCR reactions which can be used to filter the genome to predicted amplification products.

  • Xvfb - X virtual framebuffer - needed to support SplitsTree in command line mode as used in Genome Comparator.

Perl modules

These are included with most Linux distributions.

Optional packages

Installing these packages will enable extra functionality, but they are not required by the core BIGSdb package.

  • MAFFT 6.8+ - sequence alignment used by some plugins.

  • Muscle - sequence alignment used by some plugins.

  • Splitstree4 - used by GenomeComparator plugin.

  • PostGIS - needed for geographical mapping.

  • WeasyPrint - needed to generate PDF files in the Genome Reports plugin.