The NanoPipe git repository is available here.
This software was tested on Max OS X (10.10.2). The NanoPipe command line version is similar to the one that is used in the Webtool.
Requirements
To use the Pipeline, you need to have the following software installed:
- Python 2.7, from https://www.python.org/downloads/
- LAST, from http://last.cbrc.jp/
- Muscle, from http://www.drive5.com/muscle/
- poretools, from http://poretools.readthedocs.org/en/latest/
- R, from https://cran.r-project.org/
Installation Instructions
Download the NanoPipe_v*.tar.gz file and extract
it. Then, change to the directory NanoPipe_v*/
and run this command
python setup.py install
This will installl the scripts into o the standard location for third-party Python modules (more information on the locations is found here).
If you, for example, have downloaded the file to
your Downloads/ directory, you can run these commands
to install the NanoPipe scripts
cd ~/Downloads/ tar xzfv nanopipe_v*.tar.gz cd nanopipe_v*/ python setup.py install
Usage Example
To use the Script with the example data provided, run these commands
cd ~/Downloads/NanoPipe_v*/NanoPipe/example-data/ mkdir test_run cd test_run/ nanopipe -q ../plasmodium_falciparum.fq -a plasmodium
To see a help message, run
$ nanopipe -h
usage: nanopipe [-h] -q QUERY_FILE -a {dengue,plasmodium,provide}
[-t TARGET_FILE] [-f] [-V] [-l LAST_PARAMETER] [-d] [-v]
Pipeline to perform analysis on Nanopore reads.
optional arguments:
-h, --help show this help message and exit
-t TARGET_FILE, --target_file TARGET_FILE
File with target sequences.
-f, --use_all_reads Use all reads from the query data (all reads, not just
2D high quality).
-V, --version Print version information and exit.
-l LAST_PARAMETER, --last_parameter LAST_PARAMETER
Specify last parameters to be used, for example '-q8
-a13' (quotes needed).
-d, --debug Use debug mode. Will print more verbose log file.
-v, --verbose Use verbose mode.
Required arguments:
-q QUERY_FILE, --query_file QUERY_FILE
Path to file or directory with query data (in fastq or
fast5 format)
-a {dengue,plasmodium,provide}, --analysis_type {dengue,plasmodium,provide}
Which analysis task to perform. Allowed types:
['dengue', 'plasmodium', 'provide']
Output
The script creates several output files, e.g.
- consensus.fasta with the consensus sequences, based on 'majority rule'
- readspergene.tsv with the number of reads assigned to each target gene
- polymorphisms.tsv with the polymorphisms found in the target genes