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Outputs (3)

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files (2018)
Journal Article
Payne, A., Holmes, N., Rakyan, V., & Loose, M. (2018). BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files. Bioinformatics, 35(13), 2193-2198. https://doi.org/10.1093/bioinformatics/bty841

Motivation: The Oxford Nanopore Technologies (ONT) MinION is used for sequencing a wide variety of sample types with diverse methods of sample extraction. Nanopore sequencers output FAST5 files containing signal data subsequently base called to FASTQ... Read More about BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files.

Nanopore sequencing and assembly of a human genome with ultra-long reads (2018)
Journal Article
Jain, M., Koren, S., Miga, K., Quick, J., Rand, A., Sasani, T., Tyson, J., Beggs, A., Dilthey, A., Fiddes, I., Malla, S., Marriott, H., Nieto, T., O'Grady, J., Olsen, H., Pedersen, B., Rhie, A., Richardson, H., Quinlan, A., Snutch, T., …Loose, M. (2018). Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology, 36(4), 338-345. https://doi.org/10.1038/nbt.4060

© 2018 Nature Publishing Group. All rights reserved. We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, r... Read More about Nanopore sequencing and assembly of a human genome with ultra-long reads.

Virtual genome walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence (2018)
Journal Article
Evans, T., D. Johnson, A., & Loose, M. (in press). Virtual genome walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence. Scientific Reports, 8(1), Article 618. https://doi.org/10.1038/s41598-017-19128-6

Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model sp... Read More about Virtual genome walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence.