Highly parallel direct RNA sequencing on an array of nanopores
Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63 (2009).
Wu, J.Q. et al. Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol. 9, R3 (2008).
Kozarewa, I. et al. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat. Methods 6, 291–295 (2009).
Lipson, D. et al. Quantification of the yeast transcriptome by single-molecule sequencing. Nat. Biotechnol. 27, 652–658 (2009).
Mamanova, L. et al. FRT-seq: amplification-free, strand-specific transcriptome sequencing. Nat. Methods 7, 130–132 (2010).
Ozsolak, F. et al. Direct RNA sequencing. Nature 461, 814–818 (2009).
Pan, Q., Shai, O., Lee, L.J., Frey, B.J. & Blencowe, B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413–1415 (2008).
Steijger, T. et al. Assessment of transcript reconstruction methods for RNA-seq. Nat. Methods 10, 1177–1184 (2013).
Thomas, S., Underwood, J.G., Tseng, E. & Holloway, A.K. Long-read sequencing of chicken transcripts and identification of new transcript isoforms. PLoS One 9, e94650 (2014).
Vilfan, I.D. et al. Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. J. Nanobiotechnology 11, 8 (2013).
Clamer, M., Höfler, L., Mikhailova, E., Viero, G. & Bayley, H. Detection of 3′-end RNA uridylation with a protein nanopore. ACS Nano 8, 1364–1374 (2014).
Smith, A.M., Abu-Shumays, R., Akeson, M. & Bernick, D.L. Capture, unfolding, and detection of individual tRNA molecules using a nanopore device. Front. Bioeng. Biotechnol. 3, 91 (2015).
Wu, T.D. & Watanabe, C.K. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21, 1859–1875 (2005).
Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).
Byrne, A. et al. Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. Nat. Commun. 8, 16027 (2017).
Deamer, D., Akeson, M. & Branton, D. Three decades of nanopore sequencing. Nat. Biotechnol. 34, 518–524 (2016).
Oxford Nanopore Technologies Ltd. Direct RNA sequencing https://community.nanoporetech.com/protocols/direct-rna-sequencing/v/drs_9026_v1_revj_15dec201 (2016).
The HDF Group. Hierarchical data format, version 5, 1997–2017. http://www.hdfgroup.org/HDF5/.
Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009).
Larkin, M.A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007).
Li, H. & Durbin, R. Burrows–Wheeler Alignment Tool http://bio-bwa.sourceforge.net/bwa.shtml (2012).
Fariselli, P., Martelli, P.L. & Casadio, R. A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinformatics 6, S12 (2005).