GTX.CAT - High performance Genomics computing solutions

GTX.CAT develops and supplies a suite of bioinformatics secondary analysis tools that process genomics data with high computing efficiency, excellent performance, and highly consistent with BWA-GATK best practice. It offers whole-process high-performance solutions for analysis of genomic data, including quality control of raw sequencing data, DNA mapping and alignment, preprocessing of alignments, variation calling, etc.

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Product benifits
Fully functional

Support germline short variants calling
Support somantic short variants calling
Various quality control modules
Support Joint calling of large cohorts

Excellent performance

30x human WGS FASTQ-to-VCF
in an hour on a 72-threads
serverComputational expense
reduced more than 10 times

Accurate and reliable

High consistency with
BWA-GATK best practice
Reproducible result

Easy deployment

Pure software solutions
Support local and
cloud deployment

Product features
WGS/WES Germline Variants Calling
Build reference index
Compatible with BWA-MEM native index
Compatible with BWA-MEM2 native index
Support for building methylation mapping index
Mapping, Sort and Mark Duplicates
Streaming data processing, no redundant IO, process 30X human WGS data in less than 45 minutes
Support alt-aware mapping
Support mapping WGBS data
BQSR
100% coonsistent
Support for step-by-step analysis and one-click generation of quality-recalibrated BAM
BQSR of 30x human WGS data in 3 minutes
Variant calling
Support polyploid genotyping
Support on-fly BQSR
Accurate, >=99.9% consistency with GATK HaplotypeCaller
WGS/WES Somatic Variants Calling
FASTQ->BAM
Preprocess pipeline is identical to germline varaint calling
Tumor and Normal samples were processed separately
Create Panel of Normal
Based on mutect2 tumor-only mode
Support adding normal samples to database incremently
Mutect2 Somatic Calling
Support tumor-normal pair mode
Support tumor-only mode
Support process of WGS, WES, and Amplicon-based sequencing data
Somatic Variants Filtering
Support sample contamination assessment
Support learning sequecning artifacts models
Typical Application Scenarios
群体基因测序
Population Genome Sequencing
遗传疾病诊断
Genetic Disease Diagnosis
肿瘤基因检测
Oncogenetic
Testing
农业育种
Agricultural
Breeding
Comparison Test
Accuracy of germline variant calling
GTX.CAT version:v2.1.0BWA-GATK version:BWA v0.7.17 + GATK4.1.8.1
Run time of germline variant calling
Test environment: Intel(R) Xeon(R) Platinum 8358 CPU @ 2.60GHz*2，64C128T
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