genome-sampler¶
Tools for sampling from collections of genomes.
- version:
2025.02.0 - website: https://
genome -sampler .readthedocs .io - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org - citations:
- Bolyen et al., 2020
Actions¶
| Name | Type | Short Description |
|---|---|---|
| sample-random | method | Sample IDs at random. |
| sample-longitudinal | method | Sample dates uniformly across time |
| sample-neighbors | method | Sample context sequences that are near-neighbors of focal sequences. |
| sample-diversity | method | Identify a divergent collection of context sequences. |
| filter-seqs | method | Filter sequences. |
| combine-selections | method | Combine id selections. |
| mask | method | Mask alignment |
| label-seqs | method | Re-label aligned sequences |
| summarize-selections | visualizer | Summarize one or more selections. |
Artifact Classes¶
FeatureData[Selection] |
AlignmentMask |
Formats¶
IDSelectionDirFmt |
GISAIDDNAFASTAFormat |
VCFMaskFormat |
VCFMaskDirFmt |
- Bolyen, E., Dillon, M. R., Bokulich, N. A., Ladner, J. T., Larsen, B. B., Hepp, C. M., Lemmer, D., Sahl, J. W., Sanchez, A., Holdgraf, C., Sewell, C., Choudhury, A. G., Stachurski, J., McKay, M., Engelthaler, D. M., Worobey, M., Keim, P., & Gregory Caporaso, J. (2020). Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity. F1000 Research, 9(657), 657. 10.12688/f1000research.24751.1