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Workflows & Sequencing Types

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