2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2018

Marcus H Stoiber, Joshua Quick, Rob Egan, Ji Eun Lee, Susan E Celniker, Robert Neely, Nicholas Loman, Len Pennacchio, James B Brown. De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing. Technical Report bioRxiv:094672, bioRxiv, 2016.

Download preprint: not available

Download from publisher: https://doi.org/10.1101/094672

Related web page: https://nanoporetech.github.io/tombo

Bibliography entry: BibTeX


Advances in nanopore sequencing technology have enabled investigation of 
the full catalogue of covalent DNA modifications. We present the first 
algorithm for the identification of modified nucleotides without the need 
for prior training data along with the open source software implementation, 
nanoraw. Nanoraw accurately assigns contiguous raw nanopore signal to 
genomic positions, enabling novel data visualization, and increasing power 
and accuracy for the discovery of covalently modified bases in native DNA. 
Ground truth case studies utilizing synthetically methylated DNA show the 
capacity to identify three distinct methylation marks, 4mC, 5mC, and 6mA, 
in seven distinct sequence contexts without any changes to the algorithm. 
We demonstrate quantitative reproducibility simultaneously identifying 5mC 
and 6mA in native E. coli across biological replicates processed in 
different labs. Finally we propose a pipeline for the comprehensive 
discovery of DNA modifications in any genome without a priori knowledge of 
their chemical identities.