App TrainingONT: Biosphere BASE environment for "Introduction to Oxford Nanopore data analysis" training

Description

Assembly a genome using long reads from either Oxford Nanopore Technologies or Pacific Biosciences allow solve repeats and structural variants in genome of different organisms. Such technologies provide assemblies that are increased in contiguity and accuracy. This VM is used in SouthGreen training on Oxford Nanopore Technologies data, for assembly, QC and SV detection.

This training is explained using Jupyter Notebook, an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. IFB cloud appliance provides both the Jupyter Notebook and Lab environment (see explanations).

version

2022-Rabat

Tools

• Jupyter notebook/lab
• seqtk
• Guppy-cpu
• NanoPlot
• NanoComp
• Minimap2
• Diamond
• Flye
• raven-assembler
• racon
• medaka
• ragtag
• quast
• Mummer
• Assembly-Stats
• blobtools
• Bandage
• Sniffles

Contact

• Support Cloud IFB

Developers

• Julie Orjuela-Bouniol IRD SouthGreen Platform
• Francois Sabot IRD SouthGreen Platform
• Gauthier Sarah INRAe SouthGreen Platform
• Aurore Comte IRD SouthGreen Platform

App data

• Version : 20.04
• OS : Ubuntu
• OS version : 20.04

Licence

Licensed under GPLv3