Poretools - Revision history

Rf at 23:10, 23 March 2017

2017-03-23T23:10:33Z

Rf at 11:54, 13 February 2017

2017-02-13T11:54:07Z

Rf: Created page with "= Introduction Python tools for analysing fast5 files, which are output by the MinION sequencing system. = Usage = == Example == poretools fastq 5CG6210Y8Z_20160816_FNFA..."

2017-02-09T16:34:54Z

Created page with "= Introduction Python tools for analysing fast5 files, which are output by the MinION sequencing system. = Usage = == Example == poretools fastq 5CG6210Y8Z_20160816_FNFA..."

New page

= Introduction

Python tools for analysing fast5 files, which are output by the MinION sequencing system.

= Usage =

== Example ==

poretools fastq 5CG6210Y8Z_20160816_FNFAB28012_MN15120_sequencing_run_GroupB_1D_Ecoli_tune_85746_ch39_read230_strand.fast5

<ins>Explanation</ins>:
* '''poretools''' is the main tool command
* '''fastq''' is the subcommand, and it mostly defines the output that the user requires. The input is expected to be a list of fast5 filenames or a directory
* the rest of the command is actually just the fast5 filename, which is clearly very long, and is probably due to the high metadata capabilities of fast5

== Subcommand listing ==

* '''fastq''', converts fast5 to fastq format (the usual short read format with basecall quality values)
* '''fasta''', converts fast5 to fasta format (featuring only the detected basecalls)
* '''combine''', actually just renders a tar file from a group of fast5 files.
* '''yield_plot''', number of base pairs read over time (clearly important for the life of the flowcell).
* '''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''', statistics on the number of bases with respect to the reads, including size of the "winner" mentioned above
* '''hist''', histogram of read sizes
* '''nucdist''', will give nucleotide composition (%ATCGN) of a set of fast5 files
* '''qualdist''', gives the quality distribution of a set of fast5 files
* '''qualpos''', similar to the FASTQC packages gives a box-whisker plot of the quality seen over the positions of the bases.
* '''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''', time information in the fast5 file
* '''occupancy''', gives graph of pore performance based on information in a set of fast5 files.
* '''index''', tabulates all file location info and metadata
* '''metadata''', extracts metadata from a read.

= Links =
Examples of using this package can be found [http://poretools.readthedocs.io/en/latest/content/examples.html here]

@@ Line 15: / Line 15: @@
 * '''fastq''' is the subcommand, and it mostly defines the output that the user requires. The input is expected to be a list of fast5 filenames or a directory
 * the rest of the command is actually just the fast5 filename, which is clearly very long, and is probably due to the high metadata capabilities of fast5
 == Subcommand listing ==

@@ Line 1: / Line 1: @@
-= Introduction
+= Introduction =
 Python tools for analysing fast5 files, which are output by the MinION sequencing system.
 = Usage =