Using:
- vadr annotation (virus model must be selected in options)
- vardict variant caller
- coverage depth Provides summarizing files:
- png image of variant calling with annotations and coverage depths
- tsv file with all information of significant variants only
Type: Galaxy
Creators: Fabrice Touzain, This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne
Submitter: Fabrice Touzain
Using:
- vadr annotation (virus model must be selected in options)
- vardict variant caller
- coverage depth Provides summarizing files:
- png image of variant calling with annotations and coverage depths
- tsv file with all information of significant variants only
Type: Galaxy
Creators: Fabrice Touzain, This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne
Submitter: Fabrice Touzain
Using:
- vadr annotation (virus model must be selected in options)
- vardict variant caller
- coverage depth Provides summarizing files:
- png image of variant calling with annotations and coverage depths
- tsv file with all information of significant variants only (can be opened in Excel/LibreOffice)
Type: Galaxy
Creators: Fabrice Touzain, This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne
Submitter: Fabrice Touzain
Using:
- vadr annotation (virus model must be selected in options)
- vardict variant caller
- coverage depth Provides summarizing files:
- png image of variant calling with annotations and coverage depths
- tsv file with all information of significant variants only (can be opened in Excel/LibreOffice)
Type: Galaxy
Creators: Fabrice Touzain, This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne
Submitter: Fabrice Touzain
Shotgun Metagenomics Analysis
Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
Description
The input for this analysis is paired end next generation sequencing data from metagenomic samples. The workflow is designed to be modular, so that individual modules can be run depending on the nature of the metagenomics project at hand. More modules will be added as we develop them - this repo is a work in progress!
These scripts have been written ...
Type: Shell Script
Creators: Cali Willet, Rosemarie Sadsad, Tracy Chew, Smitha Sukumar, Elena Martinez, Christina Adler, Henry Lydecker, Fang Wang
Submitter: Tracy Chew