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Luke Thompson edited this page Mar 9, 2016
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| Processing step | Closed reference | Open reference | De novo |
|---|---|---|---|
| OTU picking | SortMeRNA vs GG97 v13.8 or Silva v123 | Sumaclust/SortMeRNA vs rep_set.fa | Swarm v2 |
| Taxonomy assignment | (comes with GG or Silva) | SortMeRNA | (same as open-ref) |
| Alignment | (comes with GG or Silva) | SSU-ALIGN(a) (not PyNAST) | (same as open-ref) |
| Tree building | (comes with GG or Silva) | FastTreeMP(b) | (same as open-ref) |
| Outputs (+Map) | BIOM, Taxonomy, Tree | BIOM, Taxonomy, Tree | BIOM, Taxonomy, Tree |
(a): Greg's preferred option. (b): With double precision.
| Analysis: core | Details and challenges |
|---|---|
| Alpha diversity | Calculated per sample, easily parallelizable |
| Beta diversity | Memory limitations with new algorithm (see Daniel's section below) |
| Principal coordinates | Now works with up to 50k samples using conda installation of scipy |
| Taxa summaries | Calculated per sample, easily parallelizable |
| Analysis: extended | Details and challenges |
|---|---|
| GitHub issues -- start here | https://github.com/biocore/emp/issues -- work on these, add more |
| Slides from old talks | https://github.com/biocore/emp/tree/master/presentations and Google Drive |
| IPython notebook for plots | Seaborn, Emperor, Qiime results |
| Group significance | Dependent on specific questions |
| Machine learning | Somewhat dependent on specific questions |
| Co-occurrence | Display on the VROOM with Juergen |
| Phylogenetic trees | ETE, display on the VROOM with Juergen |
| Other | Yoshiki and Jamie have code/ideas, Bobby Prill meta-analysis |