The Bacterial Isolate Genome Sequence Database (BIGSdb) is a scalable, web-accessible database system designed to store and analyse linked phenotypic and genotypic information in a computationally efficient manner. Sequence data can range from single sequence reads to multiple contigs generated by whole genome sequencing technologies. The system incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences. These loci can be further organised into schemes for isolate characterisation or for evolutionary or functional analyses.
See Jolley and Maiden 2010, BMC Bioinformatics 11:595 (http://www.biomedcentral.com/1471-2105/11/595).
You can report bugs or make enhancement requests using the issues tracker at https://github.com/kjolley/BIGSdb. The source code is also mirrored there.
The BIGSdb tool is a wonderful platform for collaborative microbial population biology and genomic epidemiology projects. It extends the concepts that made the success of MLST to the genome-wide scale. Key to its design is the separation of genotypic and isolates databases, which enables at the same time the sharing of common nomenclatures across public health agencies or research laboratories, while allowing confidentiality of isolates metadata. Our experience of the software is excellent. It is highly reliable (no bug detected so far after more than one year of usage), user friendly (despite a serious learning curve), evolves fast to extended functionality, and the support is very fast and helpful. Microbiologists with no knowledge in bioinformatics can easily use it to extract relevant information from their own microbial isolates genomes. To my knowledge there is no open-source, freely distributed equivalent software so far.