Difference between revisions of "MinION (Oxford Nanopore)"
| Line 1: | Line 1: | ||
= Introduction = | = Introduction = | ||
| − | Entirely unique sequencing method, where the flowcell is inserted into a USB container, and from there plugged into a computer. | + | Entirely unique sequencing method, where the flowcell is inserted into a USB container, and from there, plugged into a computer. |
Due to its small size in comparison with Illumina, IonTorrent and PacBio, this sequencing tool is eminently suited to field work. | Due to its small size in comparison with Illumina, IonTorrent and PacBio, this sequencing tool is eminently suited to field work. | ||
| Line 10: | Line 10: | ||
| − | Reputed advantages | + | ==Reputed advantages== |
| − | * flowcell pores good for several runs, until they die out, which they may at different times. | + | * flowcell pores good for several runs, until they die out, which they may do at different times. |
| + | ==Shortcomings== | ||
| + | * Computer, usually a laptop, needs to be continually connected to internet, and to be in high workload mode (no economy nor sleep mode allowed). | ||
The software required can be split into two groups of programs: | The software required can be split into two groups of programs: | ||
| Line 27: | Line 29: | ||
= Links = | = Links = | ||
| + | * Brian Naugton's [http://blog.booleanbiotech.com/nanopore_2016.html blog entry 11 Oct 2016] taking stock of recent advances | ||
* [http://www.nature.com/nature/journal/v530/n7589/abs/nature16996.html Nature paper 11 Feb 2016] describing Minion use in Ebola outbreak | * [http://www.nature.com/nature/journal/v530/n7589/abs/nature16996.html Nature paper 11 Feb 2016] describing Minion use in Ebola outbreak | ||
Revision as of 10:47, 2 February 2017
Introduction
Entirely unique sequencing method, where the flowcell is inserted into a USB container, and from there, plugged into a computer.
Due to its small size in comparison with Illumina, IonTorrent and PacBio, this sequencing tool is eminently suited to field work.
Overview
Reputed advantages
- flowcell pores good for several runs, until they die out, which they may do at different times.
Shortcomings
- Computer, usually a laptop, needs to be continually connected to internet, and to be in high workload mode (no economy nor sleep mode allowed).
The software required can be split into two groups of programs:
- Sequencing generation
- MinKNOW, for control of MinION device & run parameters
- Metrichor, for cloud basecalling of event data
- Chronolapse a screen image grabber for record keeping
- TeamViewer, for remote control of MinION computer
- MinoTour, live monitoring / control of run while sequencing (a collaboration with Matt Loose of Nottingham University).
- Sequence File Analysis
- Poretools, poRe Sequence extraction and data summaries (deevloped by Nick Loman and Aaron Quinlan (latter of bedtools fame)).
Links
- Brian Naugton's blog entry 11 Oct 2016 taking stock of recent advances
- Nature paper 11 Feb 2016 describing Minion use in Ebola outbreak
