On 2016 Mar 01, Mick Watson commented:

Unfortunately the authors used the incorrect function within poRe for comparison, and more appropriate ways to use the software have been in place for some time, eg:

http://www.opiniomics.org/extracting-minion-fastq-on-the-command-line-using-pore/ http://www.opiniomics.org/how-to-extract-fastq-from-the-new-minion-fast5-format-using-pore/

In fact recent work shows that poRe is incredibly fast for FASTQ extraction:

http://www.opiniomics.org/fast-parallel-access-to-data-within-minion-fast5-files/

It is a shame the authors did not make use of this functionality

Watson M, Thomson M, Risse J, Talbot R, Santoyo-Lopez J, Gharbi K, Blaxter M. poRe: an R package for the visualization and analysis of nanopore sequencing data. Bioinformatics. 2015 31(1):114-5.

On 2016 Mar 01, Mick Watson commented:

Unfortunately the authors used the incorrect function within poRe for comparison, and more appropriate ways to use the software have been in place for some time, eg:

http://www.opiniomics.org/extracting-minion-fastq-on-the-command-line-using-pore/ http://www.opiniomics.org/how-to-extract-fastq-from-the-new-minion-fast5-format-using-pore/

In fact recent work shows that poRe is incredibly fast for FASTQ extraction:

http://www.opiniomics.org/fast-parallel-access-to-data-within-minion-fast5-files/

It is a shame the authors did not make use of this functionality

Watson M, Thomson M, Risse J, Talbot R, Santoyo-Lopez J, Gharbi K, Blaxter M. poRe: an R package for the visualization and analysis of nanopore sequencing data. Bioinformatics. 2015 31(1):114-5.