VirSieve Pipeline by Zymo Research
VirSieve is a bioinformatic pipeline designed for the detection and identification of viral mutant sequences from difficult matrices such as wastewater. This pipeline is currently optimized for SARS-CoV-2, but can be adapted to many other viral species. VirSieve automates the process of alignment, primer trimming (if needed), variant calling, and variant annotation. VirSieve has an emphasis on identifying which mutations are more likely to be biologically present and which can be explained by sequencing or analysis artifacts or are otherwise potentially spurious. VirSieve is built around software containers and comes with pre-build reference data to ensure consistency between runs and between different labs.
Zymo Research Transmit Program
Zymo Research Transmit Program is a free COVID-19 public health data reporting program for uploading COVID-19 test results to the CalREDIE database at the California Department of Public Health. This COVID-19 public health data reporting program can allow uploads of results from simple reports and can be used in place of complex LIMS modifications to become compliant with public health reporting requirements in the state of California. As a free, open-source software, this COVID-19 public health data reporting program both improves epidemiological monitoring in California and allows for the potential to adapt this program to other state reporting systems.
Running Zymo Research Transmit with a Graphical Interface
In this video, we demonstrate how to install, setup, and begin uploading test results to the California Department of Public Health using Zymo Research Transmit without needing to use the Windows command console in under 10 minutes.
How to Use the Transmit Program
MIQ Score System
The MIQ Score System is an easily extensible system that contains a fully-automated, containerized microbiomics pipeline for comparing observed read abundances to expected values from a standardized microbial community with known relative abundances and manufacturing tolerances. This system is designed to be rapidly deployed through Docker in a highly-reproducible manner across different computing infrastructures and requires only information on the raw sequencing reads as input to generate a detailed report scoring accuracy relative to the standard and providing several figures that can help identify potential biases in microbiome preparation.
Bisulfite Primer Seeker
This program reflects Zymo Research’s simplification of the tedious process of bisulfite primer design. This program will help you design primers in particularly CG-rich sequences and will provide you with multiple options for amplicons that span different regions within your sequence.
FIGARO is an efficient and objective tool for optimizing microbiome rRNA gene trimming parameters. FIGARO will quickly analyze error rates in a directory of FASTQ files to determine optimal trimming parameters for high-resolution targeted microbiome sequencing pipelines, such as those utilizing DADA2 and Deblur.
Zymo's bioinformatician Michael Weinstein, PhD gives an introduction to FIGARO, an efficient and objective tool for optimizing microbiome rRNA gene trimming parameters.