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.
Swift 16S SNAPP can be cloned from https://github.com/swiftbiosciences/16S-SNAPP
Swift 16S SNAP amplifies all V1-V9 regions of 16S
Figure 1. 16S gene coverage by Swift SNAP 16S panel using a E. coli sample
- Higher accuracy in abundance estimates
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.
Figure 3. Fungal ITS1 coverage by Swift SNAP ITS panel with examples of 4 fungal species
Figure 4. Fungal ITS1 relative abundance of ZYMO I with 99.9% reads assigned to the target genera
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.
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.