Currently, OTP supports the following bioinformatic workflows:
These workflows run a number of quality control steps and report indicators that should support you in judging the quality of your data. Please refer to the documentation of the workflows for more information. For questions please contact the workflow's authors.
The workflows mostly only support paired-end data, except for the bulk RNA-seq workflow, which also supports single-end sequencing data. Furthermore, OTP supports each of these workflows only for specific sequencing types:
| Sequencing Type | Comment | Display Name (shown in GUI) | Workflows |
|---|---|---|---|
| ChIP-seq DNA sequencing | antibody target is needed | ChIP | Alignment |
| Whole exome sequencing | target-file/enrichment kit is needed | EXOME | Alignment, SNV, INDEL, Mutational signatures |
| bulk RNA-seq | RNA | RNA-seq | |
| single-cell RNA-seq | 10x_scRNA | CellRanger | |
| Whole genome sequencing | WGS | Alignment, SNV, INDEL, SV, CNV, Mutational signatures | |
| Whole genome bisulfite sequencing | WGBS | Alignment | |
| Whole genome bisulfite tagmentation sequencing | WGBS_TAG | Alignment |