Nanopore software packages for analysis (alphabetical order)
- Master Sequencer iPhone/iPad-compatible game that can be utilized as an instructional tool for demonstrating the principles behind nanopore DNA sequencing. The software is programmed by the the Drndic Lab (U Penn, USA)
- Mosaic: software based on python for nanopore current trace analysis from Kasianowicz et al. at NIST (solid-state nanopores)
- Nanolyzer: software with graphical user interface for fast and high-fidelity analysis of nanopore translocation events with arbitrarily complex substructure by Northern Nanopore Instruments (solid-state nanopores)
- Nanopore Analysis: software for nanopore current trace analysis by Yi-Tao Long's group (solid-state nanopores)
- OpenNanopore: software for nanopore current trace analysis and fitting based on Matlab by Radenovic's group (solid-state nanopores)
- Poretools: software for current trace data from Oxford Nanopore by Loman's group (biological nanopores)
- Pyth-Ion: sofware for nanopore current trace analysis based on Python programmed by Wanunu's group (solid-state nanopores)
- Transalyzer: software based on MATLAB for nanopore current trace analysis (solid-state nanopores)
Brief technical background
Label-free detection of single molecules
The idea to use ionic currents to detect particles in aqueous solutions originates from the Coulter counter, which was invented to count red blood cells more than 5 decades ago. It is a very elegant and straightforward technique that uses the brief change in resistance of an orifice due to the presence of a particle. The resistive-pulse technique has a number of advantages, including the possibility for true label-free detection and, because of this, it is widely used for cell counting. Although detection of virus particles with diameters down to 60 nm was demonstrated in the 1970s, detection of single macromolecules, like DNA, remained elusive until the 1990s. The first polymers to be detected with biological nanopores where PEG molecules, as demonstrated by Bezrukov et al. in 1994. In 1996, the first measurements of voltage-driven translocation of RNA and DNA through alpha-hemolysin were published by Kasianowicz et al. The potential to sequence DNA with nanopores kick started the field and now, almost 15 years later, there are labs around the world actively extending the limits of nanopore sensing.
Available nanopores
The detection limit for the resistive-pulse technique critically depends on the diameter and length of the sensing orifice. Classically the pores used in Coulter counters have diameters well above 10 microns. Macromolecules can only be detected using this technique with a pore with typical dimensions in the nanometre length scale. Nanopores, as we define them, are small holes in membranes that are less than 100 nm thick and have diameters well below 100 nm.
Today, there are two sources of nanopores. The 'bottom-up' method uses natural nanopores extracted from bacteria. The second approach is 'top-down' - using modern nanotechnology to fabricate nanpores in thin engineered membranes.
Biological nanopores
A very good description of model biological nanopores can be found on the nanoSEQ page.
A video describing the DNA sequencing method developed by Oxford Nanopore Technologies can be see here.
Solid-state nanopores
Descriptions of the so-called solid-state nanopores, how they are made, and what they are used for, can be found on the pages of the following reseach groups:
Cees Dekker Lab
Nynke Dekker Lab
Golovchencko and Branton Lab
Hybrid nanopores
Protein nanopores inserted into solid-state nanopores or three-dimensional nanopores made using DNA nanotechnology were also demonstrated.
Available nanopores
The detection limit for the resistive-pulse technique critically depends on the diameter and length of the sensing orifice. Classically the pores used in Coulter counters have diameters well above 10 microns. Macromolecules can only be detected using this technique with a pore with typical dimensions in the nanometre length scale. Nanopores, as we define them, are small holes in membranes that are less than 100 nm thick and have diameters well below 100 nm.
Today, there are two sources of nanopores. The 'bottom-up' method uses natural nanopores extracted from bacteria. The second approach is 'top-down' - using modern nanotechnology to fabricate nanpores in thin engineered membranes.
Biological nanopores
A very good description of model biological nanopores can be found on the nanoSEQ page.
A video describing the DNA sequencing method developed by Oxford Nanopore Technologies can be see here.
Solid-state nanopores
Descriptions of the so-called solid-state nanopores, how they are made, and what they are used for, can be found on the pages of the following reseach groups:
Cees Dekker Lab
Nynke Dekker Lab
Golovchencko and Branton Lab
Hybrid nanopores
Protein nanopores inserted into solid-state nanopores or three-dimensional nanopores made using DNA nanotechnology were also demonstrated.
