Bioinformatics Resources

Analyze complex NGS data faster and easier using Swift Bioinformatics Resources

varsome

For Swift Human Amplicon Panels and Swift Hyb

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 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 or VCF files into the secure cloud-based VarSome platform and leverage the rich set of features available to analyze and annotate the resulting data.

HOW DOES IT WORK?

varsome big data

(1) Add a Varsome token (AL-VS48) to your order.  In order to process data from 48 samples. Ask about a demo of the software and evaluation specials!
(2) Upload FASTQ or VCF file. VarSome accepts FASTQ and 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!

(3) 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.
(4) 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!
(5) Generate Reports. Once you have narrowed down the list of variants of interest, you can proceed with the generation of a 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.
TECHNICAL NOTE

Primerclip™: A Tool for Trimming Primer Sequences

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PANEL-SPECIFIC BIOINFORMATICS FILES AND SEQUENCING DATA
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SAMPLE SHEETS

Sample Sheets can be found on product pages within the Protocol, Tools and Technical Notes modal

“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

bioinformatics

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Swift Resources for Data Analysis of 16S+ITS panels (ACCEL and SNAP)

Bioinformatics analysis solutions to SNAP 16S panel

Swift 16S SNAPP Open Source Pipeline is Swift’s latest solution for studying microbial communities using Swift SNAP 16S panel (see tech note).  This pipeline starts with demultiplexed FASTQ files by a simple command and delivers the community composition table and reference phylogenetic tree. Not only does this pipeline encapsulate the standard but complex tasks, it is equipped for properly handling multi-V region amplicons to capture their collective advantages over the single amplicon 16S approach. Swift 16S SNAPP generates consensus sequences from multi-V region amplicons, and provides higher resolving power in quantifying microbial compositions.

 Swift 16S SNAPP uses DADA2 for identifying amplicon sequence variants (ASVs) and RDP Classifier to taxonomic assignments.

SNAP-APP for 16S multi-amplicon analysis

Swift 16S SNAPP can be cloned from https://github.com/swiftbiosciences/16S-SNAPP

swift 16S SNAP github

Swift 16S SNAP amplifies all V1-V9 regions of 16S

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Figure 1. 16S gene coverage by Swift SNAP 16S panel using a E. coli sample

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Figure 2.  Genus-level composition of ATCC® MSA-1003TM mixed genomic DNA generated using Swift SNAP 16S panel and characterized using 16S SNAPP

  • Higher accuracy in abundance estimates

  • Greater number of identified reads

Bioinformatics analysis solutions to SNAP ITS panel

ITS analysis workflow, q2wkflow_ITS_v3, (Qiime 2-based) is a simple script for studying fungal communities using Swift SNAP ITS panel. This pipeline starts with demultiplexed FASTQ files by a simple command and delivers the fungal community abundance tables.

q2wkflow_ITS_v3 uses DADA2 for identifying amplicon sequence variants (ASVs) and UNITE-trained Naïve Baysian Classifier for taxonomic assignments.

bioinformatics Swift SNAP ITS
Figure 3.  Fungal ITS1 coverage by Swift SNAP ITS panel with examples of 4 fungal species

composition zymoI

Figure 4.  Fungal ITS1 relative abundance of ZYMO I with 99.9% reads assigned to the target genera

Example data sequenced from ZymoBIOMICS Microbial DNA Standard using SNAP ITS panel can be downloaded from here.

Swift Resources for Data Analysis of Accel-Amplicon™Panels

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.

Primerclip vs. Cloud-Based Analysis decision tree

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.

Please visit Github to download Primerclip.

SWIFT AMPLICON ANALYSIS SOLUTIONS

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.

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