Index switching causes “spreading-of-signal” among multiplexed samples in Illumina HiSeq 4000 DNA sequencing
By Rahul Sinha, Geoffrey M. Stanley, G. Gulati, Camille Ezran, K. Travaglini, Eric Wei, C. Chan, Ahmad N. Nabhan, Tianying Su, Rachel M. Morganti and 7 more. bioRxiv, 2017
213 citations recorded by the source corpus.
Subfields: Cancer Research, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/1269aa9b8d2b5f4b9ffadf88db96ebf19c77e882
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Citations in the corpus
- Benchmarking Metagenomics Tools for Taxonomic Classification. (2019, background): “Cross-talk between multiplexed samples on Illumina flow-cells (especially notable on more recent sequencers that use patterned flow cells) can generate biological false positives at low abundances (Sinha et al., 2017).”
- Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads (2016, background): “As some contamination is possible in sequencing read sets (particularly when multiplexing, which is a common strategy for bacterial isolate sequencing on Illumina[11]), Unicycler then removes contigs with a depth of less than half the median graph depth, unless doing so would create a dead end.”
- Transient leaf endophytes are the most active fungi in 1-year-old beech leaf litter (2017, methodology): “To account for potential errors due to tag switching (Carlsen et al. 2012; Sinha et al. 2017), we applied an abundance threshold for each OTU, only above which it was considered to be present in the respective sample (see Supplementary file S1 for details, Fig.”
- The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages (2019, methodology): “To circumvent known index-hopping issues with the HiSeq 4000 platform (Sinha et al., 2017), cell barcodes common to more than one sample were removed from the aggregated count matrix.”