Sentieon
This topic explains how to use Sentieon, a third-party software package integrated into Alibaba Cloud Genomics.
Sentieon
Sentieon®, founded in 2014, has a team of experts specializing in algorithms, software, and system tuning. They develop highly optimized bioinformatics applications that won challenges organized by precisionFDA and are widely used by leading institutions, including universities and hospitals.
Prerequisites
Sentieon is commercially licensed software. You must purchase a license directly from the official vendor.
In your task parameters, set the license_server field to your license server address. For assistance with server configuration, submit a ticket to contact us.
Features
The Genomics platform integrates the full Sentieon software suite, including the Sentieon® DNASeq®, TNseq®, and TNscope® series. It supports the following common analysis use cases:
Alignment | Sentieon® BWA matches BWA-MEM with >2X speedup. |
Germline SNV/INDEL variant calling | DNAseq®: PrecisionFDA award-winning software. Matches GATK 3.3-4.1, and without downsampling, delivering results up to 10x faster with 100% consistency. DNAscope: Improved accuracy and genome characterization. Machine learning-enhanced filtering produces top variant calling accuracy. |
Somatic SNV/INDEL variant calling | TNseq®: Matches MuTect, MuTect2 v3.8 - 4.0 without downsampling for higher accuracy and improved detections of low allelic fraction variants. TNscope®: Winner of ICGC-TCGA DREAM challenge. Improved accuracy, machine learning-enhanced filtering. Supports molecular barcodes and unique molecular identifiers. |
Structural variant calling | Germline and somatic SV calling, including translocations, inversions, duplications and large INDELs. |
Joint calling | Supports large-cohort joint calling of over 200,000 WGS samples directly from gVCF and without intermediate steps. |
BCL-FASTQ tool | Sentieon®'s external library accelerates BCL to FASTQ conversion by 1.5 - 2x. |
RNA variant calling | Complies with GATK RNAseq variant calling best practices. |
Procedure
The Genomics platform simplifies the use of Sentieon by providing public applications. This approach retains all of Sentieon's native functionalities and supports custom development. To analyze genomic data or build your own accelerated applications, use one of the following methods:
Install Sentieon analysis workflows directly from the App Repository:
You can also open an analysis workflow to select a different version:
Alibaba Cloud Genomics provides the "201911", "202010.02", "202112.05", "202112.06", and "202308" versions of Sentieon in all available regions.
Create a custom Sentieon workflow:
You can also customize your own Sentieon application based on the Sentieon workflow in public applications by specifying the Sentieon version in the software field of the runtime attribute in the WDL. The command block supports various native Sentieon usages.
runtime {
software: "sentieon:202308"
}For example:
For details about Sentieon's functionality, see Commands and usage of the Sentieon software.