1. Within-Run Cross-Contamination in Deep Sequencing Applications on the Illumina MiSeq

croiconference.org/abstract/withi…
2. Common Contaminants in NGS
Until an effective strategy is found to eliminate contaminants from sequencing runs, novel sequences detected in such runs should be scrutinized by qPCR analysis to ensure they originate from specimens rather than the lab
journals.plos.org/plosone/articl…
3. From trash to treasure: detecting unexpected contamination in unmapped NGS data
bmcbioinformatics.biomedcentral.com/articles/10.11…

Here we propose DecontaMiner, a tool to unravel the presence of contaminating sequences among the unmapped reads
4. Virus expression detection reveals RNA-sequencing contamination in TCGA bmcgenomics.biomedcentral.com/articles/10.11…
Ballenghien et al. found 80% of samples from a large-scale sequencing experiment had evidence of cross-contamination, which likely occurred in the sequencing center
5. Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions

bmcbiol.biomedcentral.com/articles/10.11…
6. Detection of Viral Pathogens With Multiplex Nanopore MinION Sequencing: Be Careful With Cross-Talk
frontiersin.org/articles/10.33…
7. Illumina COVIDSeq Test Instructions for Use
The Illumina® COVIDSeq™ Test is a Next-Generation Sequencing (NGS) in vitro diagnostic test on the Illumina
Sequencing System,intended for the qualitative detection of SARS-CoV-2 RNA from BALF specimens
fda.gov/media/138776/d…

• • •

Missing some Tweet in this thread? You can try to force a refresh
 

Keep Current with Billy Bostickson 🏴👁&👁 🆓

Billy Bostickson 🏴👁&👁 🆓 Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @BillyBostickson

7 Mar
Compilation Thread on ORF8 ORF8 or Fate?
1. ZLS (2018):
"Considering the variability of orf8 in bats, civets and humans, investigating the function of orf8 is a priority, particularly the contribution of these different variants to viral pathogenesis."
2. ORF8 or Fate?
"In addition to receptor binding, proteolytic cleavage of S & potentially other mutations that affect virion & trimer stability may be important for virus transmissibility in different hosts, & these factors need to be studied further."
nature.com/articles/s4157…
3. ORF8 or Fate?
Overwhelmingly these viruses had mutations or
29 deletions in ORF8 - associated with reduced replicative fitness of the virus.. may be associated with host adaptation
via @CarltheChippy
382-nt deletion during early evolution of SARS-CoV
biorxiv.org/content/10.110…
Read 30 tweets
7 Mar
(A and B Sequence & structural properties of insert PRRA (D) Sequence similarity between close neighborhood of PRRA insert, neurotoxin motifs Y674QTQTNSPRRAR685, homologous to Ophiophagus (cobra) & Bungarus genera & 3 RABV strains & HIV-1 gp120 superantigenic motif in last row Image
Study on Ribonuclease From Snake Venom of Zhejiang Cobra (Naja naja atra)
ZHANG Gon-jin
Wuhan Institute of Virology,Academia Sinica
zoores.ac.cn/article/id/1281 Image
Read 4 tweets
5 Mar
@Daoyu15 @franciscodeasis @spectropan @ResearchGate @TheSeeker268 STRANGE TO SEE THIS IN Wuhan Hu-1
Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1
Clostridium_difficile
Bat coronavirus BM48-31/BGR/2008
Human coronavirus 229E
@Daoyu15 @franciscodeasis @spectropan @ResearchGate @TheSeeker268 A Bulgarian Bat Virus mentioned in Lam et al:
Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China
biorxiv.org/content/10.110…
Read 10 tweets
28 Feb
AN ASSESSMENT OF CHINA’S BIOLOGICAL WARFARE CAPABILITIES AND NEED FOR GLOBAL APPROACH TO BIO-SECURITY Part 1 (Indian Analysis, May 2020) researchgate.net/publication/34…
China's Biological Timeline
media.nti.org/pdfs/china_bio…
Read 5 tweets
28 Feb
Same covid-19 mutations are appearing in different places, which may or may not be strange....
41,000 mutations documented in 880 lineages.
Most in spike protein
What explains it?
Read 18 tweets

Did Thread Reader help you today?

Support us! We are indie developers!


This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Too expensive? Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal Become our Patreon

Thank you for your support!

Follow Us on Twitter!