tibljТуберкулез и болезни легкихTuberculosis and Lung Diseases2075-12302542-1506Медицинские знания и технологии10.21292/2075-1230-2017-95-6-41-44tiblj-1012Research ArticleОРИГИНАЛЬНЫЕ СТАТЬИORIGINAL ARTICLESНОВОЕ ПРОГРАММНОЕ ОБЕСПЕЧЕНИЕ ДЛЯ ОБРАБОТКИ ДАННЫХ ПОЛНЫХ ГЕНОМОВ МИКОБАКТЕРИЙ ТУБЕРКУЛЕЗАNEW SOFTWARE FOR PROCESSING DATA OF ENTIRE GENOME OF MYCOBACTERIUM TUBERCULOSISСпринджукМ. В.SprindzhukM. V.

Спринджук Матвей Владимирович - научный сотрудник, разработчик программного обеспечения.

220012, Минск, ул. Сурганова, д. 6, тел.: +375 29 567 10 73

Matvey V. Sprindzhuk - Researcher, Developer of the software.

6, Surganova St., Minsk, Belarus, 220012, Phone: +375 29 567 10 73

msprindzhuk@mail.ruТитовЛ. П.TitovL. P.

Титов Леонид Петрович - РНПЦ эпидемиологии и микробиологии, доктор медицинских наук, профессор, член-корреспондент НАН Беларуси, академик РАМН, заведующий лабораторией иммунологии и микробиологии.

220114, Минск, ул. Филимонова, д. 23. тел.: +375 29 626 58 66

Leonid P. Titov - Republican Research and Practical Center for Epidemiology and Microbiology, Doctor of Medical Sciences, Professor, Correspondent Member of NAS of Belarus, Academician of RAMS, Head of Immunological and Microbiological Laboratory.

23, Filimonova St., Minsk, Belarus Republic, 220114, Phone: +375 29 626 58 66

leonidtitov@tut.byЗалуцкаяО. М.ZаlutskаyaO. M.

Залуцкая Оксана  Михайловна - врач-бактериолог РНПЦ фтизиатрии  и пульмонологии.

220035, Минск, Долгиновский тракт, д. 157, тел.: +375 29 325 36 06

Oksana M. Zalutskaya – Bacteriologist, Republic Scientific and Practical Center of Pulmonology and Tuberculosis.

157, Dolginovsky Road, Minsk, Belarus Republic, 220035, Phone: +375 29 325 36 06

akasana@inbox.ruСкрягинА. Е.SkryaginA. E.

Cкрягин Александр Егорович - Белорусский государственный медицинский университет, кандидат медицинских наук, доцент кафедры анестезиологии и реаниматологии, врач-реаниматолог.

220116, Минск, пр. Дзержинского, д. 83, тел.: +375 29 679 98 71

Aleksander E. Skryagin - Belorussian State Medical University, Candidate of Medical Sciences, Associate Professor of Anesthesiology and Intensive Care Department, Intensive Care Physician.

83, Dzerzhinskogo Ave., Belarus Republic, 220116, Phone: +375 29 679 98 71

aliaksandr_skrahin@tut.byСкрягинаА. М.SkryaginаA. M.

Скрягина  Алена Михайловна - доктор медицинских наук, профессор, заместитель директора РНПЦ фтизиатрии  и пульмонологии.

220035, Минск, Долгиновский тракт, д. 157, тел.: +375 29 184 07 83

Alena M. Skryagina - Doctor of Medical Sciences, Professor, Deputy Director, Republic Scientific and Practical Center of Pulmonology and Tuberculosis.

157, Dolginovsky Road, Minsk, Belarus Republic, 220035, Phone: +375 29 184 07 83

СергеевР. С.SergeevR. S.

Сергеев  Роман Сергеевич - научный сотрудник, математик.

220012, Минск, ул. Сурганова, д. 6, тел.: +375 29 557 41 67

Roman S. Sergeev - Researcher, Mathematician.

6, Surganova St., Minsk, Belarus, 220012, Phone: +375 29 557 41 67

roma.sergeev@gmail.comОбъединенный институт проблем информатики Национальной академии наук БеларусиБеларусьUnited Institute of Informatics ProblemsBelarus2017060720179564144Copyright © Спринджук М.В., Титов Л.П., Залуцкая О.М., Скрягин А.Е., Скрягина А.М., Сергеев Р.С., 20172017Спринджук М.В., Титов Л.П., Залуцкая О.М., Скрягин А.Е., Скрягина А.М., Сергеев Р.С.Sprindzhuk M.V., Titov L.P., Zаlutskаya O.M., Skryagin A.E., Skryaginа A.M., Sergeev R.S.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://www.tibl-journal.com/jour/article/view/1012

В статье представлено  описание  разработанного  программного  обеспечения,  предназначенного для обработки данных полных геномов микобактерии туберкулеза человека.

The article describes the software developed for processing of data of entire genomes of human tuberculous mycobacteria.

туберкулезгеномикапрограммное обеспечениеtuberculosisgenomicssoftwareГранты научных проектов CRDF, ОИПИ НАН Беларуси, РНПЦ микробиологии и эпидемиологии г. Минска; В. А. Горбунов, доцент; А. П. Кончиц, доцентGrants from CRDF, United Institute of Informatics Problems of Belarus, the Republican Research and Practical Center for Epidemiology and Microbiology of Minsk; V.A. Gorbunov and A.P. Konchits, Associate ProfessorsReferencesBradley P., Gordon N. C., Walker T. M., Dunn L., Heys S. et al. Corrigendum: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis // Nat. Commun. – 2016. – Vol. 7. – P. 11465.Bradley P., Gordon N.C., Walker T.M., Dunn L., Heys S. et al. Corrigendum: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat. Commun., 2016, vol. 7, pp. 11465.Bradley P., Gordon N. C., Walker T. M., Dunn L., Heys S. et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis // Nat. Commun. – 2015. – Vol. 6. – P. 10063.Bradley P., Gordon N.C., Walker T.M., Dunn L., Heys S. et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat. Commun., 2015, vol. 6, pp. 10063.Burland T. G. DNASTAR's Lasergene sequence analysis software // Methods Mol. Biol. – 2000. – Vol. 132. – P. 71-91.Burland T.G. DNASTAR's Lasergene sequence analysis software. Methods Mol. Biol., 2000, vol. 132, pp. 71-91.Cingolani P., Platts A., Wang le L., Coon M., Nguyen T. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3 // Fly (Austin). – 2012. – Vol. 6, № 2. – P. 80-92.Cingolani P., Platts A., Wang le L., Coon M., Nguyen T. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin), 2012, vol. 6, no. 2, pp. 80-92.Clewley J. P. GENEMAN of LASERGENE // Methods Mol. Biol. – 1997. – Vol. 70. – P. 189-196.Clewley J.P. GENEMAN of LASERGENE. Methods Mol. Biol., 1997, vol. 70, pp. 189-196.Clewley J. P. Macintosh sequence analysis software. DNAStar's LaserGene // Mol. Biotechnol. – 1995. – Vol. 3, № 3. – P. 221-224.Clewley J.P. Macintosh sequence analysis software. DNAStar's LaserGene. Mol. Biotechnol., 1995, vol. 3, no. 3, pp. 221-224.Clewley J. P., Arnold C. MEGALIGN. The multiple alignment module of LASERGENE // Methods Mol. Biol. – 1997. – Vol. 70. – P. 119-129.Clewley J.P., Arnold C. MEGALIGN. The multiple alignment module of LASERGENE. Methods Mol. Biol., 1997, vol. 70, pp. 119-29.Downey T. Analysis of a multifactor microarray study using Partek genomics solution // Methods Enzymol. – 2006. – Vol. 411. – P. 256-70.Downey T. Analysis of a multifactor microarray study using Partek genomics solution. Methods Enzymol., 2006, vol. 411, pp. 256-70.Farhat M. R., Sultana R., Iartchouk O., Bozeman S., Galagan J. et al. Genetic determinants of drug resistance in Mycobacterium tuberculosis and their diagnostic value // Am. J. Respir. Crit. Care Med. – 2016. – P. 652-657.Farhat M.R., Sultana R., Iartchouk O., Bozeman S., Galagan J. et al. Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. Am. J. Respir. Crit. Care Med., 2016, pp. 652-657.Ford C., Yusim K., Ioerger T., Feng S., Chase M. et al. Mycobacterium tuberculosis – heterogeneity revealed through whole genome sequencing // Tuberculosis (Edinb). – 2012. – Vol. 92, № 3. – P. 194-201.Ford C., Yusim K., Ioerger T., Feng S., Chase M. et al. Mycobacterium tuberculosis – heterogeneity revealed through whole genome sequencing. Tuberculosis (Edinb.), 2012, vol. 92, no. 3, pp. 194-201.Ford C. B., Lin P. L., Chase M. R., Shah R. R., Iartchouk O. et al. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection // Nat. Genet. – 2011. – Vol. 43, № 5. – P. 482-486.Ford C.B., Lin P.L., Chase M.R., Shah R.R., Iartchouk O. et al. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat. Genet., 2011, vol. 43, no. 5, pp. 482-486.Gaifer Z., Babiker A., Rizavi D. Epidemiology of drug-resistant tuberculosis in a tertiary care center in Oman, 2006-2015 // Oman. Med. J. – 2017. – Vol. 32, № 1. – P. 36-40.Gaifer Z., Babiker A., Rizavi D. Epidemiology of Drug-resistant Tuberculosis in a Tertiary Care Center in Oman, 2006-2015. Oman. Med. J., 2017, vol. 32, no. 1, pp. 36-40.Gilbert G. L., Sintchenko V. The use of mycobacterial interspersed repetitive unit typing and whole genome sequencing to inform tuberculosis prevention and control activities // N S W Public Health Bull. – 2013. – Vol. 24, № 1. – P. 10-14.Gilbert G.L., Sintchenko V. The use of mycobacterial interspersed repetitive unit typing and whole genome sequencing to inform tuberculosis prevention and control activities. N S W Public Health Bull., 2013, vol. 24, no. 1, pp. 10-14.Glynn J. R., Guerra-Assuncao J. A., Houben R. M., Sichali L., Mzembe T. et al. Whole genome sequencing shows a low proportion of tuberculosis disease is attributable to known close contacts in rural malawi // PLoS One. – 2015. – Vol. 10, № 7. – P. e0132840.Glynn J.R., Guerra-Assuncao J.A., Houben R.M., Sichali L., Mzembe T. et al. Whole genome sequencing shows a low proportion of tuberculosis disease is attributable to known close contacts in rural malawi. PLoS One, 2015, vol. 10, no. 7, pp. e0132840.Grayson B. L., Aune T. M. A comparison of genomic copy number calls by Partek Genomics Suite, Genotyping Console and Birdsuite algorithms to quantitative PCR // BioData Min. – 2011. – Vol. 4. – P. 8.Grayson B.L., Aune T.M. A comparison of genomic copy number calls by Partek Genomics Suite, Genotyping Console and Birdsuite algorithms to quantitative PCR. BioData Min., 2011, vol. 4, pp. 8.Guthrie J. L., Gardy J. L. A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis // Ann. N Y Acad Sci. – 2017. – Vol. 1388, № 1. – P. 59-77.Guthrie J.L., Gardy J.L. A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis. Ann. N Y Acad Sci., 2017, vol. 1388, no. 1, pp. 59-77.Hiltemann S., Mei H., de Hollander M., Palli I., van der Spek P. et al. CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy // Gigascience. – 2014. – Vol. 3, № 1. – P. 1.Hiltemann S., Mei H., de Hollander M., Palli I., van der Spek P. et al. CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy. Gigascience, 2014, vol. 3, no. 1, pp. 1.Madduri R. K., Sulakhe D., Lacinski L., Liu B., Rodriguez A. et al. Experiences Building Globus Genomics: A Next-Generation Sequencing Analysis Service using Galaxy, Globus, and Amazon Web Services // Concurr Comput. – 2014. – Vol. 26, № 13. – P. 2266-2279.Madduri R.K., Sulakhe D., Lacinski L., Liu B., Rodriguez A. et al. Experiences Building Globus Genomics: A Next-Generation Sequencing Analysis Service using Galaxy, Globus, and Amazon Web Services. Concurr Comput., 2014, vol. 26, no. 13, pp. 2266-2279.Pedersen B. S., Layer R. M., Quinlan A. R. Vcfanno: fast, flexible annotation of genetic variants // Genome Biol. – 2016. – Vol. 17, № 1. – P. 118.Pedersen B.S., Layer R.M., Quinlan A.R. Vcfanno: fast, flexible annotation of genetic variants. Genome Biol., 2016, vol. 17, no. 1, pp. 118.Steiner A., Stucki D., Coscolla M., Borrell S., Gagneux S. KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes // BMC Genomics. – 2014. – Vol. 15. – P. 881.Steiner A., Stucki D., Coscolla M., Borrell S., Gagneux S. KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes. BMC Genomics, 2014, vol. 15, pp. 881.

The authors declare that there are no conflicts of interest present.