https://github.com/sanojpunchihewa/f5n
Genopo a.k.a. F5N - A nanopore sequencing analysis toolkit for Android smartphones https://nanoporetech.com
https://github.com/sanojpunchihewa/f5n
android bioinformatics-pipeline minimap2 mobile-genomics nanopolish portable-genomics samtools sequence-alignment toolkit
Last synced: 4 months ago
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Genopo a.k.a. F5N - A nanopore sequencing analysis toolkit for Android smartphones https://nanoporetech.com
- Host: GitHub
- URL: https://github.com/sanojpunchihewa/f5n
- Owner: SanojPunchihewa
- License: mit
- Created: 2019-09-20T06:50:03.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2021-08-02T05:35:01.000Z (over 4 years ago)
- Last Synced: 2024-04-14T14:02:18.694Z (almost 2 years ago)
- Topics: android, bioinformatics-pipeline, minimap2, mobile-genomics, nanopolish, portable-genomics, samtools, sequence-alignment, toolkit
- Language: Java
- Homepage:
- Size: 123 MB
- Stars: 10
- Watchers: 3
- Forks: 7
- Open Issues: 18
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://travis-ci.com/SanojPunchihewa/f5n)
## Genopo a.k.a. F5N is a nanopore sequencing analysis toolkit for Android smartphones
### Overview
Genopo can run following analysis tools on mobile devices [more details](https://github.com/SanojPunchihewa/f5n/blob/master/docs/Supplementary_materials.pdf)
1. [minimap2](https://github.com/lh3/minimap2)
2. [samtools](https://github.com/samtools/samtools)
3. [f5c](https://github.com/hasindu2008/f5c)
4. [nanopolish](https://github.com/jts/nanopolish)
5. [bcftools](https://github.com/samtools/bcftools)
6. [artic_c](https://github.com/hiruna72/artic_c)
7. [bioawk](https://github.com/lh3/bioawk)
In particular, Genopo has buit in pipelines for
1. [Methylation Calling](https://hasindu2008.github.io/f5c/docs/commands#calling-methylation)
2. [Event Alignment](https://hasindu2008.github.io/f5c/docs/commands#aligning-events)
2. [Variant Calling](https://nanopolish.readthedocs.io/en/latest/manual.html#variants)
3. [Consensus Building](http://samtools.github.io/bcftools/bcftools.html#consensus)
4. nCoV-2019 novel coronavirus bioinformatics protocol [(Artic pipeline)](https://artic.network/ncov-2019)
### Real-time sequence analysis (in alpha phase)
Real-time methylation calling on nanopore sequencing batch datasets is experimented.
More details can be found at [here](https://github.com/AnjanaSenanayake/f5n_server)
### Installation
Genopo application can be obtained from:
[Google Play](https://play.google.com/store/apps/details?id=com.mobilegenomics.f5n)
Additionally you can get development builds from Github releases
Chose `ARCHITECTURE` to be `armeabi-v7a` or `arm64-v8a`. To find what is the `ARCHITECTURE` of your phone the easiest way is to google it. Once you download the apk copy it to your phone and install.
```sh
VERSION=0.0.4
ARCHITECTURE=armeabi-v7a
wget "https://github.com/SanojPunchihewa/f5n/releases/download/$VERSION/mobilegenomics-f5n-v$VERSION-$ARCHITECTURE-release.apk"
```
Signature keys of builds are different. Before you switch the installation source, you will have to uninstall the existing Genopo application.
### Demo
Configure single/multiple tools | Help
:-------------------------:|:-------------------------:
 | 
#### Connecting to F5N server, downloading, running and sending results
### Datasets
You can use publicly available [datasets](https://github.com/nanopore-wgs-consortium/NA12878/blob/master/Genome.md)
### How to contribute
Please contribute to our work by testing,debugging and developing our product. A guide to how to contribute is available [here](https://github.com/MarcDiethelm/contributing/blob/master/README.md)
### Submit an issue
Please submit your issues [here](https://github.com/SanojPunchihewa/f5n/issues). Make sure your issue is not an existing one.
If a similar issue already exists comment or vote under the existing issue.