Performance comparison of benchtop high-throughput sequencing platforms

By Nicholas J. Loman, Raju V. Misra, Timothy Dallman, C. Constantinidou, S. Gharbia, J. Wain, M. Pallen. Nature Biotechnology, 2012

1,384 citations recorded by the source corpus.

Subfields: Clinical Biochemistry, Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4e352253d467d7f1fa87fa59f140c2aff866a7ae

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Citations in the corpus

Culture-independent molecular tools for soil and rhizosphere microbiology (2013, background): “400 Mb -Inadequate for SNP or mutation analysis [156–158]”
Generations of Sequencing Technologies: From First to Next Generation (2017, background): “The major disadvantage is the difficulty of interpreting the homopolymer sequences (more than 6 bp) [21,36] which causes insertion and deletion (indel) error with a rate about ~1%.”
FunGene: the functional gene pipeline and repository (2013, result): “The rates for the ﬁrst two compare favorably with the claimed error rate for the 454 Titanium platform (1.07%; Gilles et al., 2011), while the error rate for BUK2 is similar to the claimed error rate for the junior platform (1.88%; Loman et al., 2012).”
Measuring the activity of protein variants on a large scale using deep mutational scanning (2014, background): “Although sequencing quality has improved, error rates as high as 1% are possible 30,31 .”
A first look at the Oxford Nanopore MinION sequencer (2014, background): “Illumina’s sequencing platforms currently attain the best balance between read lengths, error rates and cost (Loman et al. 2012).”
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities (2017, methodology): “Illumina (MiSeq and HiSeq) sequencing platforms at the moment outperform other models for accuracy (Loman et al., 2012), and multiplexing samples is usually achieved by the incorporation of sample-specific nucleotide indices and sequencing adapters during PCR amplification.”
Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter? (2017, background): “The cost per sample may vary depending on the HTS technologies used (Loman et al. 2012), but Stein et al. (2014) showed that DNA metabarcoding can be a valid economic solution for biomonitoring programs at the national scale.”
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies (2012, background): “For a detailed review of sequencing technologies please refer to Loman et al. (12).”