New release available now (V1.2.4): Fungi database

[Rachid]

Dear CLARK users!

A new release has been posted and is now available on the CLARK website! Now included:

Fungi database

In addition to the database of bacterial/archaeal, viruses and human genomes, we've included a list of 29 reference genomes to represent a database of fungi.

These 29 references sequences from RefSeq correspond to organisms associated with known hospital-acquired infections and other nosocomial diseases (See the references below). 

This release also include some bug fixes (especially for the database of viral sequences from RefSeq). Please refer to the README file and the CLARK website for more information. 

Thank you all for your interest and please feel free to suggest new features or comments for improving the software!

Cheers,

Rachid

References

• Nucci, M., & Anaissie, E. (2007). Fusarium infections in immunocompromised patients. Clinical Microbiology Reviews, 20(4), 695-704.
• Cortez, K.J., E. Roilides, F. Quiroz-Telles, J. Meletiadis, C. Antachopoulos et al., 2008 Infections caused by Scedosporium spp. Clin Microbiol Rev 21 (1):157-197. 
• Rodriguez-Tudela, J.L., J. Berenguer, J. Guarro, A.S. Kantarcioglu, R. Horre et al., 2009 Epidemiology and outcome of Scedosporium prolificans infection, a review of 162 cases. Med Mycol 47 (4):359-370. 
• Wessolossky, M., Welch, V. L., Sen, A., Babu, T. M., & Luke, D. R. (2013). Invasive Aspergillus infections in hospitalized patients with chronic lung disease. Infection and drug resistance, 6, 33. doi:10.2147/IDR.S43069.
• Lackner, M., G.S. de Hoog, L. Yang, L. Ferreira Moreno, S.A. Ahmed et al., 2014 Proposed nomenclature for Pseudallescheria, Scedosporium and related genera. Fungal Diversity 67 (1):1-10. 
• Chatterjee, S., Alampalli, S. V., Nageshan, R. K., Chettiar, S. T., Joshi, S., & Tatu, U. S. (2015). Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris. BMC genomics, 16(1), 686.