Thread by @BillyBostickson

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…