Tool for digital spoligotyping of MTB strains from Illumina read data
Latest version can be found: http://genomeview.org/jenkins/lorikeet/
A recent version of Java is required.
Download the package, unzip wherever and run.
In the directory where you unzipped the package use the following command:
java -jar lorikeet-<version>.jar spoligotype
Follow the on-screen instructions.
Input data needs to be in BAM, SAM or FASTQ format
A Galaxy wrapper is available in the Galaxy toolshed
https://github.com/galaxyproject/tools-iuc/tree/master/tools/lorikeet
Please cite this paper if you use this method
Cohen*, K., Abeel*, T., Manson McGuire, A., Desjardins, C., Munsamy, V., Shea, T., Walker, B., Bantubani, N., Almeida, D., Alvarado, L., Chapman, S., Mvelase, N., Duffy, E., Fitzgerald, M., Govender, P., Gujja, S., Hamilton, S., Howarth, C., Larimer, J., Maharaj, K., Pearson, M., Priest, M., Zeng, Q., Padayatchi, N., Grosset, J., Young, S., Wortman, J., Mlisana, K., O'Donnell, M., Birren, B., Bishai, W., Pym+, A., Earl+, A. 2015. Evolution of extensively drug-resistant tuberculosis over four decades: whole genome sequencing and dating analysis of Mycobacterium tuberculosis isolates from KwaZulu-Natal. PLOS Medicine. 12 (9): e1001880 [PubMed: 26418737]
Peter van Heusden (Sanbi)