Analyze complex NGS data faster and easier using Swift Bioinformatics Resources
NGS laboratories need better, faster tools to analyze large amounts of sequencing data. With advancements in throughput, speed and breadth of applications, it’s critical to have a wide range of tools to accommodate your needs and expertise.
Swift is building a community of tools and commercial partners to simplify data analysis. Starting with targeted gene sequencing, we’re enabling solutions whether you prefer open- source tools or plug-and-play commercial solutions.
A host of bioinformatics resources are available to help with data analysis for Accel-Amplicon and Accel-Amplicon Plus Cancer Panels. Please review the following Selection Guide to determine the best bioinformatics approach for your application.
Bioinformatics Resource Library for Accel-Amplicon™ and Accel-Amplicon Plus™Panels
Sequencing data generated from Accel-Amplicon Panels can be analyzed using various publicly available tools. It is important to note that these panels are comprised of overlapping (tiled) amplicons, which provide continuous coverage of regions of interest in a single-tube format. This unique capability enables interrogation of clinically-relevant variants in compromised and dilute samples such as FFPE and cfDNA. As a result of our library preparation process, synthetic primer sequences will be present in the sequenced reads, and these primer sequences must be bioinformatically trimmed from overlapping amplicon reads to ensure accurate variant calling. Primers can be trimmed with a Swift open-source primer trimming tool called Primerclip. For more information, please consult our Technical Note.
”We were really satisfied with the speed and availability of the entire bioinformatics team at Swift Biosciences. Despite the thousands of kilometers that separate us, they are always there in case of question or for punctual help. Working with them was a real pleasure.”
Séverine Arcioni, Institut Central Hôpital du Valais | ICHV · Genetique
Swift Amplicon targeted panels facilitate the generation of NGS data for oncology and disease research by enriching and sequencing genes of interest from challenging samples in a cost-effective manner. Following Swift’s 2 hour DNA-to-Library Prep workflow and sequencing, the data generated must be computationally aligned to a reference genome and variant calling performed to assess the status of genetic mutations, insertions, and deletions present in the sample. With the VarSome platform from Saphetor, users of Swift Amplicon panels can simply upload their sequencing FASTQ files straight from the sequencer into the secure cloud-based VarSome platform and leverage the rich set of features available to analyze and annotate the resulting data.
How does VarSome work?
(1) Upload FASTQ or VCF file. VarSome accepts FASTQ (straight from sequencer) or VCF files as single samples or in batches. You can upload the data easily and securely through the web interface or harness VarSome’s powerful API for automated and secure data transfer. Once the data are uploaded, you can start the analysis.
(2) Annotate and Classify. The robust pipeline is capable of analyzing whole genomes, exomes, and gene panels, for individual samples, trios, families, and cohorts in minutes. VarSome leverages the massive cross-referenced knowledge base of the free VarSome and also offers access to licensed databases.
(3) Explore the Intuitive Web Portal. VarSome Clinical’s feature-rich and intuitive web interface allows filtering variants according to pathogenicity, ACMG classification, allele frequency, gene list or phenotype, to name a few! Dynamic and algorithmic filters allow you to perform simple or advanced filtering, like segregation analysis, identification of de novo variants or variants in imprinted genes, and much more!
(4) Generate Reports. Once you have narrowed down the list of variants of interest, you can proceed with the generation of a customizable PDF report, which includes all the details of your variants, including literature references and your custom comments. The layout of the report can be fully customized according to your unique policy.