lorikeet

Tool for digital spoligotyping of MTB strains from Illumina read data

Latest version can be found: http://genomeview.org/jenkins/lorikeet/

Installation

A recent version of Java is required.

Download the package, unzip wherever and run.

Running

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

Galaxy wrapper

A Galaxy wrapper is available in the Galaxy toolshed

https://github.com/galaxyproject/tools-iuc/tree/master/tools/lorikeet

Citation

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]

Contributors

Peter van Heusden (Sanbi)