TRAPID 2.0

TRAPID 2.0 is a web application for the annotation and exploration of de novo transcriptomes, available here.

Documentation

• General documentation
• Tutorials
• FAQ
• Overview of all used third-party tools

Requirements

All you need to use TRAPID 2.0 is any modern web browser with JavaScript enabled.

TRAPID 2.0 is freely accessible for academic use. If you have a commercial interest in the platform, or would like to use TRAPID for commercial purposes, please contact us.

Support

If you experience a bug, or if you have any question, remark or suggestion, please contact us or open an issue.

Installation

The public instance of TRAPID 2.0 is available here. Follow the below instructions in case you want to install TRAPID 2.0.

Hardware requirements

1. MySQL server (5.7.17 or higher) with sufficient storage
2. PHP web server (e.g. Apache)
3. Sufficient storage for resources (e.g. Kaiju and DIAMOND indices, NCBI taxonomy files, Rfam data) and experiment temporary data.

Software requirements

1. General:

   • PHP (7 or higher)
   • Perl (5.14 or higher), with the Inifiles module installed.
   • Python 2.7 (for now!). Python module dependencies are listed in app/scripts/python/requirements.txt and can be installed via pip (e.g. pip install -r requirements.txt).
   • SunGridEngine (SGE) for the computing cluster on which TRAPID jobs run
   • Java (1.6 or higher)

2. Initial processing:

   • Kaiju
   • DIAMOND
   • Infernal
   • eggNOG-mapper version 1

3. Multiple sequence alignments:

   • MAFFT
   • MUSCLE

4. Phylogeny:

   • FastTree2
   • IQ-TREE
   • PhyML
   • RaxML

Note: the exact versions of the third-party tools used within TRAPID can be found in the documentation.

Databases

This repository contains the web application and the data processing code (see app/scripts/). TRAPID additionally requires at least two MySQL databases to run:

1. The TRAPID database, that stores experiment data (e.g. transcripts, functional annotation, taxonomy, gene/RNA families, ...), taxonomy data, and other configuration data.
2. A reference database (or more), that stores biological sequences, functional annotation, and gene family information for a set of reference species. The reference database is used throughout the web application as well as during the initial processing phase to derive gene family and functional annotations for the processed transcripts (in the case of eggNOG, eggNOG-mapper is used for these two last steps instead).

SQL schemes and example data for the required databases can be found here (TRAPID FTP).

Installation steps

1. Install all the programs listed in the Software requirements section.
2. Create the TRAPID and the reference database (here corresponding to eggNOG 4.5), and use the SQL dumps to create and populate the tables.
   • trapid_db_dump.sql: TRAPID database. Note that the value in db_name (data_sources table) must match the name given to the reference database.
   • reference_db_eggnog_dump.sql: reference database (eggNOG 4.5 data).
   • Create database account(s) used to access the databases.
3. Create or download necessary files/resources:
   • DIAMOND indices, based on the annotation table of the reference database.
   • Kaiju index and accompanying NCBI taxonomy data.
   • Rfam library of CMs and clan information files (links for version 14.1).
4. Clone or download the repository.
5. Change configuration:
   • Create and edit all necessary INI files in the app/scripts/ini_files, starting from the available templates (*.default, to rename as *.ini).
   • Change the database configuration in app/Config/database.php.
6. Edit the .htaccess file in the root directory as appropriate.