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NGS Software


SureDesign is a web-based application that harnesses the flexibility of SurePrint oligo manufacturing technology for the creation of custom NGS target enrichment libraries, CGH microarray designs, and FISH probes.

SureDesign, free to all registered users, has an intuitive design wizard that creates custom panels specific to research needs, as well as for cross-validation using multiple applications.


  • NGS Target Enrichment: Create custom SureSelect or HaloPlex target enrichment library designs based on the targets you want to sequence.

  • Define regions of interest and select probes based on target genes, genomic coordinates, or selection parameters.

  • CGH, ChIP-on-chip, DNA Methylation: Create custom CGH designs with various layouts, from 8 x 15 K up to 1 x 1 M.

  • CRISPR Guide RNAs: Find gRNAs that target CRISPR sites within any sequence.

  • Identify potential target candidate sites in the input or selected background.

  • Download ready to order DNA sequence templates.

  • FISH Probes: Input gene names, accession IDs, or genomic coordinates to create custom break apart, dual fusion or single probes.

  • Rapidly validate results by creating the same assay on a FISH probe and an array or target enrichment library.

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NGS Software


SureCall is a research desktop application combining both novel and widely accepted opensource algorithms for end-to-end NGS data analysis from alignment to categorization and annotation of mutations, supporting Agilent Target Enrichment applications.

SureCall provides four different types of analysis: Single, Pair, Trio, and OneSeq CNV and Mutation analysis. The SNPPET SNP caller is an Agilent algorithm, which is optimal for detecting low-frequency variants with high sensitivity and specificity.


  • From alignment of raw data to categorization and annotation of mutations in three simple steps

  • Supports four different types of analysis: Single Sample, Tumor-Normal, Trio and OneSeq CNV and Mutation Analysis

  • Supports variant annotation from many public sources, including NCBI, COSMIC, PubMed, ClinVar and custom annotation

  • Utilize single/duplex molecular barcodes (MBC) to remove false positives and accurately detect variants down to ≤1% variant allele frequency

  • Addresses the needs of clinical researchers from analysis to reporting out of their target enrichment NGS data, eliminating data analysis as a bottleneck

NGS Software


The Agilent Genomics NextGen Toolkit (AGeNT) is a Java-based software module that processes the read sequences from targeted high-throughput sequencing data generated by sequencing Agilent SureSelect and HaloPlex libraries.

The Trimmer utility of the AGeNT module processes the read sequences to identify and remove the adaptor sequences and extracts dual molecular barcodes (for SureSelect XT HS2).

The LocatIt utility of the AGeNT module processes the Molecular Barcode (MBC) information from HaloPlex HS, SureSelect XT HS, and SureSelect XT HS2 Illumina sequencing runs with options to either mark or merge duplicate reads and output in BAM file format.


  • Consists of flexible command line tools for NGS data processing, ready to be run on Linux shells as well as Windows and Mac command line with minimal configuration.

  • Processes the read sequences of Agilent’s Target Enrichment libraries to identify and remove the adaptor sequences

  • Deduplicate reads using the Molecular Barcode (MBC) information from HaloPlex HS, SureSelect XT HS, and SureSelect XT HS2 Illumina sequencing runs.


Additional Software Requirements

  • Java version 8 or later

Current Software Version

  • 2.0

Latest Version Available

  • Yes


  • ≥8RAM GB

Operating System Requirements

  • RedHat Enterprise Linux 8.0

  • Windows 10 Enterprise

  • macOS Mojave

Clinical Informatics Platform

Alissa Align & Call

Alissa Align & Call is the scalable NGS data analysis module on the Alissa Clinical Informatics Platform that analyzes raw sequencing data. It seamlessly integrates with Alissa Interpret* for clinical-grade variant assessment and reports, reducing workflow complexity and time—from raw data to draft report.

The high-quality read-mapping of Align & Call enables efficient alignment to called variants for detection, annotation, and visualization using proprietary algorithms optimized for Agilent SureSelect, HaloPlex, and OneSeq target enrichment libraries and reagents.

*Alissa Interpret is compatible with all secondary data analysis tools that produce standard VCF files.


  • Scalable NGS secondary data analysis solution designed with the routine lab user in mind.

  • Optimized algorithms for SNPs/Indels, CNV and cnLOH and Translocation variant analysis.

  • Superior visualization tools to aid reviewing called variants in context.

  • Generates QC assessment files to inform confidence in assay results.

  • Assignment of user-specific roles, managed by a workgroup administrator, that define the permitted user privileges for each account in the workgroup.

  • Seamless integration and navigation with data interpretation module, Alissa Interpret, when a licensed account is available.

  • Built and deployed under an ISO 27001 certified environment.

Clinical Informatics Platform

Alissa Interpret Research

Alissa Interpret Research is a web-based informatics solution that enables clinical research labs to efficiently triage, curate and report genomic variants. It automates NGS and CGH array workflows from variant filtration and annotation, through curation and classification, to draft lab report.

Designed with clinical research labs in mind, our web-based solution provides access to a wealth of annotation sources and databases. It supports building a bespoke curated variant database and features a range of in-depth analytic tools for variant assessment.


  • Reduces turnaround time of variant triage, classification, and reporting through standardization and automation of efficient variant interpretation and ease in drafting of actionable reports.

  • Unlocks direct access to variant annotations with the integration of best-in-class community-driven and premium third-party knowledge bases.

  • Built for clinical research from the ground up, Alissa Interpret enables informed decisions along with full reproducibility and complete traceability.

  • Enables single-workflow variant assessment for both inherited disease and somatic assays, including SNPs, indels, CNVs, LOH, and translocations/fusion genes.

  • Facilitates analysis of molecular profiles in the context of phenotype or tumor tissue type.

  • Delivers a scalable, high-security cloud-based SaaS solution with minimal requirements on local IT infrastructure.

  • Scales from small panels to exomes and whole genomes with compatibility to support any design, sequencer or assay.

  • With our API, integrate seamlessly with LIMS systems and BioIT pipelines; set-up and maintenance delivered as a service or through your IT.

  • Access a wealth of annotation sources and databases, including JAX-CKB for the most current information on actional variants from the Jackson Laboratory Clinical Knowledgebase (JAX-CKBTM).

  • Supported by a team of experts who partner with you during deployment and as your lab and volumes grow.

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