Primer Monitor Update - 2023-08

CDC TOAST Hours 2022-07-01 BA.4, BA.5 primer-variant overlap update

NGS Club Talk 2022-02-22

The precise sequence of the viruses infecting our community members can inform our response. I’ll share some results and details about the workflow we use to prepare, sequence, and reason about the viruses identified in our CLIA screening.

CDC TOAST 2021-12-03

High mutation rates observed in RNA viruses like SARS-CoV-2 have been shown to disrupt amplification based detection and sequencing methods. To produce a more variant-resistant sequencing method, we identified all variants observed more than 1000 times in consensus sequences present in GISAID. We produced thousands of multiplex PCR designs and identified those that were least affected by known variants. During product development and scale-up, we periodically evaluated designs comparing with variants that arose during product development. NEB VarSkip designs exhibited fewer primer site variant overlaps than ARTICv4 or Midnight primer schemes.

VarSkip sequencing - SFAF 2021

High mutation rates observed in RNA viruses like SARS-CoV-2 have been shown to disrupt amplification based detection and sequencing methods. To produce a more variant-resistant sequencing method, we identified all variants observed more than 1000 times in consensus sequences present in GISAID. We produced thousands of multiplex PCR designs and identified those that were least affected by known variants. During product development and scale-up, we periodically evaluated designs comparing with variants that arose during product development. NEB VarSkip designs exhibited fewer primer site variant overlaps than ARTICv4 or Midnight primer schemes.

CDC TOAST Hours 2021-06-24 Primer Monitor, Varskip Sequencing

CDC Spheres 2021-06-23 Primer Monitor, Varskip Sequencing

SFAF2020 Unique Molecular Indices Improve RNA-seq Experiments

Copy of Improving Transcriptome Analysis with Molecular Indices and Galaxy

Improving Transcriptome Analysis with Molecular Indices and Galaxy

Analysis of Immune Sequence Data in Galaxy

We have made the pRESTO suite of tools available in Galaxy for use with the NEBNext AbSeq immune sequencing kit

GCC 2017 RNA-seq at NEB

White Tailed Deer Genome - Josh McCoy 2016

SeqResults - GCC2016

Meta-data aware, high-throuput sequence result aggregation

White Tailed Deer Genome - ISCB NGS 2016