Bioinformatics

Software

Tools used for data analysis, before giving samples to students include:

• SeekDeep (Hathaway et al. 2017)

  • we used this to trim sequences, assemble similar sequences, and create a contig for each group of similar sequences

• RDP classifier (Cole et al. 2014)

  • we used this to search a database of plant ITS sequences, identify best match taxa, and statistically determine whether we could classify each contig to the species, genus, or family level

• Krona (Ondov et al. 2011)

  • we used this to make pie charts visualizing the species contents of each supplement

Cole, J. R., Q. Wang, J. A. Fish, B. Chai, D. M. McGarrell, Y. Sun, C. T. Brown, A. Porras-Alfaro, C. R. Kuske, and J. M. Tiedje. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis Nucleic Acids Research 42:D633-D642.

Hathaway, N.J., C.M. Parobek, J.J. Juliano, J.A. Bailey. 2018. SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing. Nucleic Acids Research 46:e21.

Ondov, B.D., N.H. Bergman, and A.M. Phillippy. 2011. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 12:385.

Contact us

If you would like details on how we analyzed the raw sequence data, and would like to do it yourself, please contact Naoki Takebayashi <ntakebayashi@alaska.edu>

You will need access to a Linux computer