Russian version English version
Volume 13   Issue 1   Year 2018
Bukin Yu.S., Buzoleva L.S., Golozubova Y.S., Galachyants Yu.P.

New Procedure of Raw Illumina MiSeq Data Filtering For the Amplicon Metagenomic Libraries

Mathematical Biology & Bioinformatics. 2018;13(1):159-168.

doi: 10.17537/2018.13.159.



  1. Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114-2120. doi: 10.1093/bioinformatics/btu170
  2. Chun J., Kim K.Y., Lee J.H., Choi Y. The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer. BMC Microbiology. 2010;10(1):101. doi: 10.1186/1471-2180-10-101
  3. Dixon P. VEGAN, a package of R functions for community ecology. Journal of Vegetation Science. 2003;14(6):927-930. doi: 10.1111/j.1654-1103.2003.tb02228.x
  4. Fosso B., Santamaria M., Marzano M., Alonso-Alemany D., Valiente G., Donvito G., Monaco A., Notarangelo P., Pesole G. BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS. BMC Bioinformatics. 2015;16(1):203. doi: 10.1186/s12859-015-0595-z
  5. Katoh K., Toh H. Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics. 2010;26(15):1899-1900. doi: 10.1093/bioinformatics/btq224
  6. Kim M., Lee, K.H., Yoon S.W., Kim B.S., Chun J., Yi H. Analytical tools and databases for metagenomics in the next-generation sequencing era. Genomics & Informatics. 2013. V. 11;3:102-113. doi: 10.5808/GI.2013.11.3.102
  7. Magoč T., Salzberg S.L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27(21):2957-2963. doi: 10.1093/bioinformatics/btr507
  8. Morgan M., Anders S., Lawrence M., Aboyoun P., Pages H., Gentleman R. ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics. 2009;25(19):2607-2608. doi: 10.1093/bioinformatics/btp450
  9. Petrosino J.F., Highlander S., Luna R.A., Gibbs R.A., Versalovic J. Metagenomic pyrosequencing and microbial identification. Clinical Chemistry. 2009;55(5):856-866. doi: 10.1373/clinchem.2008.107565
  10. Quail M.A., Smith M., Coupland P., Otto T.D., Harris S.R., Connor T.R., Bertoni A., Swerdlow H.P., Gu Y. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012;13(1):341. doi: 10.1186/1471-2164-13-341
  11. Quast C., Pruesse E., Yilmaz P., Gerken J., Schweer T., Yarza P., Peplies J., Glöckner F.O. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research. 2013;41(D1):D590-D596. doi: 10.1093/nar/gks1219
  12. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology. 2009;75(23):7537-7541. doi: 10.1128/AEM.01541-09
  13. Smith E.P., van Belle G. Nonparametric estimation of species richness. Biometrics. 1984;40(1):119-129. doi: 10.2307/2530750
  14. Tennant R.K., Sambles C.M., Diffey G.E., Moore K.A., Love J. Metagenomic Analysis of Silage. Journal of Visualized Experiments: JoVE. 2017;119. doi: 10.3791/54936
  15. Zhou J., Wu L., Deng Y., Zhi X., Jiang Y.H., Tu Q., Yang Y. Reproducibility and quantitation of amplicon sequencing-based detection. The ISME Journal. 2011;5(8):1303-1313. doi: 10.1038/ismej.2011.11
Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2018.13.159
published in English

Abstract (eng.)
Abstract (rus.)
Full text (eng., pdf)


  Copyright IMPB RAS © 2005-2024