Pipeline info & flowchart - mooreryan/ZetaHunter GitHub Wiki

Flow chart showing the ZetaHunter pipeline. Third-party tools used in the pipeline are indicated to the left.

ZetaHunter pipeline flowchart

Overview

The default pipeline of ZetaHunter takes SINA-aligned 16S rRNA gene sequences and processes them in this order:

  1. Sequences are checked for chimeras using mothur's uchime algorithm.
  2. SortmeRNA is used to cluster new sequences to the reference database based on genetic distance (closed reference binning).
  3. The remaining sequences are clustered into novel OTUs by average neighbor OTU clustering with mothur.
  4. Summary, biom (table showing OTU abundance per sample), and OTU network files are exported for use.

This pipeline is an implementation of open-reference OTU picking similar to the one found in QIIME

Citations

  • Kopylova, E, L Noé, and H Touzet. 2012. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics, 28:3211–3217. doi:10.1093/bioinformatics/bts611
  • Edgar, RC, BJ Haas, JC Clemente, C Quince, and R Knight. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27:2194–2200. doi:10.1093/bioinformatics/btr381
  • Navas-Molina, JA, JM Peralta-Sánchez, A González, PJ McMurdie, Y Vázquez- Baeza, Z Xu, LK Ursell, C Lauber, H Zhou, SJ Song, J Huntley, GL Ackermann, D Berg-Lyons, S Holmes, JG Caporaso, and R Knight. 2013. Advancing our understanding of the human microbiome using QIIME. Methods Enzymol., 531:371–444. doi:10.1016/B978-0-12-407863-5.00019-8
  • Schloss PD, SL Westcott, T Ryabin, JR Hall, M Hartmann, EB Hollister, RA Lesniewski, BB Oakley, DH Parks, CJ Robinson, JW Sahl, B Stres, GG Thallinger, DJ van Horn, and CF Weber. 2009. Introducing mothur: open-source, platform- independent, community-supported soft- ware for describing and comparing microbial communities. Appl. Environ. Microbiol., 75:7537–7541. doi:10.1128/AEM.01541-09