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AliTVTeam / AliTV

Visualize whole genome alignments as linear maps
https://alitvteam.github.io/AliTV/d3/AliTV.html
MIT License
69 stars 11 forks source link

readme

** Tutorial Read the documentation at [[http://alitv.readthedocs.io/en/latest/index.html][readthedocs]].

** Dependencies

** Installation You do not need to install anything to try the interactive visualization of AliTV. Just navigate to the [[https://alitvteam.github.io/AliTV/d3/AliTV.html][demo]] page to try all the features on an example dataset (seven chloroplast genomes). You can also import your own json files on that page. When loading your own data into AliTV it is not transferred to a server but remains on your local machine.

If you want to generate the json file for your genomes you can use the command line script alitv.pl as follows:

+BEGIN_EXAMPLE

Install perl dependencies e.g. with cpan, cpanm or package manager (example: apt)

apt install libyaml-perl libhash-merge-perl bioperl

git clone --recursive https://github.com/AliTVTeam/AliTV

+END_EXAMPLE

** Usage AliTV.pl can be called directly on your input files or in advanced mode supplying a yaml configuration file. The output is a json object as required by the visualization part of AliTV (see [[https://alitvteam.github.io/AliTV/d3/doc/AliTV.html][details]]) in the file .json (project can be set via command line parameter, otherwise a random name is generated). For more details about ~alitv.pl~ please see [[https://github.com/AliTVTeam/AliTV-perl-interface/blob/master/doc/alitv.md][the documentation]].

Simple mode: Just supply your files and redirect to json file

+BEGIN_EXAMPLE

cd AliTV-perl-interface perl bin/alitv.pl --project simple data/chloroset/*.fasta

+END_EXAMPLE

Advanced mode: Supply a config yaml file

+BEGIN_EXAMPLE

cd AliTV-perl-interface perl bin/alitv.pl --project advanced data/chloroset/input.yml

+END_EXAMPLE

** Input Input for the simple mode should be in one of the [[http://bioperl.org/howtos/SeqIO_HOWTO.html#item5][Bioperl supported formats]] (currently 42 different). Annotation files can be supplied in tsv format (have to be specified in the yml file, [[https://github.com/AliTVTeam/AliTV-perl-interface/blob/master/data/chloroset/ndh.tsv][example file for ndh genes]]). Documentation for the yaml file is soon to be added for now consult this [[https://github.com/AliTVTeam/AliTV-perl-interface/blob/master/data/chloroset/input.yml][example file]] for usage information.

** Output By default, AliTV generates a configuration file (yaml format) if none is supplied, a log file and a json string on standard out. The json can then be visualized with AliTV on the [[https://alitvteam.github.io/AliTV/d3/AliTV.html][demo]] page or locally in [[d3/AliTV.html]]. The format of the json file is specified in the source documentation relevant members are "conf", "data", and "filters".

** Homepage For further information visit the [[http://alitvteam.github.io/AliTV][homepage]].

** Citing AliTV

An article about AliTV has been published in [[https://peerj.com/articles/cs-116/][PeerJ Computer Science]] [[https://peerj.com/articles/cs-116/][https://img.shields.io/badge/DOI-10.7717%2Fpeerj--cs.116-blue.svg]] Please cite this article if you use AliTV in your project. Additionally the software in any specific version can be cited via its zenodo doi, latest: [[https://zenodo.org/badge/latestdoi/12731/AliTVTeam/AliTV][https://zenodo.org/badge/12731/AliTVTeam/AliTV.svg]]

Please also cite:

** Contact If you have any questions or encounter problems or potential bugs, don't hesitate to contact us. Either report [[https://github.com/AliTVTeam/AliTV/issues][issues]] on github or write an email to:

** License [[https://github.com/AliTVTeam/AliTV/blob/master/LICENSE][https://img.shields.io/github/license/mashape/apistatus.svg]]

AliTV itself is available under MIT license. The licenses of included libraries might differ, please see [[LICENSES/README.org]] for details. ** Build [[https://travis-ci.org/AliTVTeam/AliTV/][https://travis-ci.org/AliTVTeam/AliTV.svg?branch=master]] [[https://coveralls.io/github/AliTVTeam/AliTV?branch=master][https://coveralls.io/repos/github/AliTVTeam/AliTV/badge.svg?branch=master]]

** Repo Status [[https://www.repostatus.org/#inactive][https://www.repostatus.org/badges/latest/inactive.svg]] Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.

** Changelog *** Next release

+TITLE: AliTV

+AUTHOR: Markus Ankenbrand

+EMAIL: markus.ankenbrand@uni-wuerzburg.de

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