MinION (Oxford Nanopore) - Revision history

Rf at 09:55, 17 October 2017

2017-10-17T09:55:26Z

Rf at 16:35, 9 February 2017

2017-02-09T16:35:41Z

Rf at 16:54, 8 February 2017

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Rf at 13:35, 8 February 2017

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Rf at 16:49, 3 February 2017

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Rf at 15:43, 3 February 2017

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@@ Line 98: / Line 98: @@
 * [https://github.com/mw55309/EG_MinION_2016/blob/master/02_Data_Extraction_QC.md key aspects] of the fast5 file format
 * [http://porecamp.github.io/2016/ Porecamp 2016, training course page]
 =Notes=
 <references />

@@ Line 87: / Line 87: @@
 * '''Poretools''', poRe Sequence extraction and data summaries (developed by Nick Loman and Aaron Quinlan (latter of bedtools fame)). This is installed on the marvin cluster with version number 0.6.0 as of Jan 2017.
 * '''poRe''', by Mick Watson, very similar to poretools, but for the R statistics platform. Found [https://sourceforge.net/projects/rpore/files/0.20 here]
 = Links =

@@ Line 77: / Line 77: @@
 * It seems that MinKNOW needs the Metrichor agent to be running, although this is not entirely clear.
 * Traditionally they require Windows. But it both packages are now avilable for MacOSX.
-* ONT also have the MinKNOW software for Linux, namely Ubuntu Trusty 14.04 (which actually is the latest Bio Linux installation) but there is no Ubuntu version of Metrichor, so this does not seem useful.
+* ONT also have the MinKNOW software for Linux, namely Ubuntu Trusty 14.04 (which actually is the latest Bio Linux installation) but there is no Ubuntu version of Metrichor, so this does not seem useful. However on Wed 8 Feb 2017, and Ubuntu version of the user agent for Ubuntu was released.
 * Metrichor has its own website at www.metrichor.com. Authentication seems to be done via the nanopore website however.

@@ Line 65: / Line 65: @@
 The software required can be split into two groups of programs:
-* Sequencing generation
+== Sequencing generation ==
-** '''MinKNOW''', for control of MinION device & run parameters
+* '''MinKNOW''', for control of MinION device & run parameters
-** '''Metrichor''', for cloud basecalling of event data
+* '''Metrichor''', for cloud basecalling of event data
-** '''Chronolapse''' a screen image grabber for record keeping
+* '''Chronolapse''' a screen image grabber for record keeping
-** '''TeamViewer''', for remote control of MinION computer
+* '''TeamViewer''', for remote control of MinION computer
-** '''MinoTour''', live monitoring / control of run while sequencing (a collaboration with Matt Loose of Nottingham University).
+* '''MinoTour''', live monitoring / control of run while sequencing (a collaboration with Matt Loose of Nottingham University).
-** '''MinUP''', a Matt Loose tool allowing uploading of data for the MinoTour program
+* '''MinUP''', a Matt Loose tool allowing uploading of data for the MinoTour program
 The main product of these tools is the fast5 file format. This format has good metadata capabilities, though the extent and usefulness of this metadata depends on how the experiment is run.
@@ Line 77: / Line 84: @@
 However, direct monitoring of the base calls is also now possible, due to Matt Loose at Nottingham University, using the MinoTour platform. This requires an external server, one of which is available at University of Nottingham, but it is also possible to set one up internally if need be.
-* Sequence File Analysis
+== Sequence File Analysis ==
-** '''Poretools''', poRe Sequence extraction and data summaries (developed by Nick Loman and Aaron Quinlan (latter of bedtools fame)). This is installed on the marvin cluster with version number 0.6.0 as of Jan 2017.
+* '''Poretools''', poRe Sequence extraction and data summaries (developed by Nick Loman and Aaron Quinlan (latter of bedtools fame)). This is installed on the marvin cluster with version number 0.6.0 as of Jan 2017.
-** '''poRe''', by Mick Watson, very similar to poretools, but for the R statistics platform. Found [https://sourceforge.net/projects/rpore/files/0.20 here]
+* '''poRe''', by Mick Watson, very similar to poretools, but for the R statistics platform. Found [https://sourceforge.net/projects/rpore/files/0.20 here]
 == Examples of poretools usage ==

@@ Line 113: / Line 113: @@
 = Links =
 * Brian Naughton'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
 * [https://github.com/mw55309/EG_MinION_2016/blob/master/02_Data_Extraction_QC.md key aspects] of the fast5 file format
 * [http://porecamp.github.io/2016/ Porecamp 2016, training course page]
 =Notes=
 <references />

@@ Line 105: / Line 105: @@
 * '''tabular''', gives the raw details of each read: its size, name, sequence and quality.
 * '''events''', reads out the event information stored in the fast5 file.
-* times
+* '''times''', time information in the fast5 file
-* occupancy
+* '''occupancy''', gives graph of pore performance based on information in a set of fast5 files.
-* index
+* '''index''', tabulates all file location info and metadata
 Examples of using this package can be found [http://poretools.readthedocs.io/en/latest/content/examples.html here]

@@ Line 102: / Line 102: @@
 * '''nucdist''', will give nucleotide composition (%ATCGN) of a set of fast5 files
 * '''qualdist''', gives the quality distribution of a set of fast5 files
-* qualpos
+* '''qualpos''', similar to the FASTQC packages gives a box-whisker plot of the quality seen over the positions of the bases.
-* tabular
+* '''tabular''', gives the raw details of each read: its size, name, sequence and quality.
-* events
+* '''events''', reads out the event information stored in the fast5 file.
 * times
 * occupancy

@@ Line 98: / Line 98: @@
 * '''squiggle''', graphs the signal recorded by the pore as the DNA passed through it. This is all held by the fast5 file.
 * '''winner''', gives the longest read
-* '''stats''', read size statistics
+* '''stats''', statistics on the number of bases with respect to the reads, including size of the "winner" mentioned above
 * '''hist''', histogram of read sizes
-* '''nucdist''' nucleotide composition
+* '''nucdist''', will give nucleotide composition (%ATCGN) of a set of fast5 files
-* '''qualdist''',quality score composition.
+* '''qualdist''', gives the quality distribution of a set of fast5 files
 * qualpos
 * tabular