Sentieon is a commercial solution to process genomics data with high computing efficiency, fast turnaround time, exceptional accuracy, and 100% consistency.
If Sentieon is available, use this --sentieon params to enable with Sarek to use some Sentieon Analysis Pipelines & Tools.
Please refer to the nf-core/configs repository on how to make a pipeline-specific configuration file based on the munin-sarek specific configuration file.
Or ask us on the nf-core Slack on the following channels: #sarek or #configs.
The following Sentieon Analysis Pipelines & Tools are available within Sarek.
Sentieon BWA matches BWA-MEM with > 2X speedup.
This tool is enabled by default within Sarek if --sentieon is specified and if the pipeline is started with the mapping step.
Precision FDA award-winning software. Matches GATK 3.3-4.1, and without down-sampling. Results up to 10x faster and 100% consistent every time.
This tool is enabled within Sarek if --sentieon is specified and if --tools DNAseq is specified cf --tools.
Improved accuracy and genome characterization. Machine learning enhanced filtering producing top variant calling accuracy.
This tool is enabled within Sarek if --sentieon is specified and if --tools DNAscope is specified cf --tools.
Winner of ICGC-TCGA DREAM challenge. Improved accuracy, machine learning enhanced filtering. Supports molecular barcodes and unique molecular identifiers.
This tool is enabled within Sarek if --sentieon is specified and if --tools TNscope is specified cf --tools.
Germline and somatic SV calling, including translocations, inversions, duplications and large INDELs
This tool is enabled within Sarek if --sentieon is specified and if --tools DNAscope is specified cf --tools.
Adds the following tools for the --tools options: DNAseq, DNAscope and TNscope.
For main usage of tools, follow the usage/tools documentation.
With --sentieon the following tools options are also available within Sarek: DNAseq, DNAscope and TNscope.