A new experience published with Oxford Nanopore

[AntonioRFranco]

http://jac.oxfordjournals.org/conten....full.pdf+html

[luc]

from this Judge et al paper ( Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes):
".... Under these mapping criteria only 25% of the MinION reads aligned to the reference, although this provided an even mapping depth across the genome (Table 1). Error rates were substantially higher in the mapped MinION reads compared with the two other technologies, with short indels being much more common in the MinION data (Table 1). ... "

[NextGenSeq]

from this Judge et al paper ( Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes):
".... Under these mapping criteria only 25% of the MinION reads aligned to the reference, although this provided an even mapping depth across the genome (Table 1). Error rates were substantially higher in the mapped MinION reads compared with the two other technologies, with short indels being much more common in the MinION data (Table 1). ... "

Yes, indels are a problem since 5 bp are read at a time. If a homopolymer is longer than this it can't be resolved (currently). ONT admits this and is working on solutions to it.