Team I Webserver Group: Difference between revisions
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=='''Functionalities'''== | =='''Functionalities'''== | ||
===Genome Assembly=== | ===Genome Assembly=== | ||
*Performs de-novo assembly with FastQ files as input | |||
*Runs following tools by default: | |||
**fastp: read pre-processing | |||
**Unicycler: Genome assembly | |||
*Options: | |||
**Perform read preprocessing | |||
**Kmer-size | |||
**Spades as alternative assembly method | |||
*The input FastQ files must be paired-end reads | |||
*Outputs FASTA file | |||
*Visualisation: Quast output | |||
===Gene Prediction=== | ===Gene Prediction=== | ||
===Functional Annotation=== | ===Functional Annotation=== | ||
Revision as of 03:19, 18 April 2020
Members: Devishi Kesar, Shuheng Gan, Winnie Zheng, Priya Narayanan, Aaron Pfennig
Introduction
Background
Objective
- Provide a comprehensive, automated platform to analyze E.coli isolates in order to predict virulence factors and outbreak cluster
- Functionalities of the webserver:
- Identify virulence factors/microbial resistance and outbreak response for provided isolates
- Allow data upload at each step of outline pipeline
- Visualize findings in a comprehensible way
- Design
- Intuitive usage
- Provide only essential options
WebServer
- Structure
- Access to Webserver
Here is Link to access our webserver:
Functionalities
Genome Assembly
- Performs de-novo assembly with FastQ files as input
- Runs following tools by default:
- fastp: read pre-processing
- Unicycler: Genome assembly
- Options:
- Perform read preprocessing
- Kmer-size
- Spades as alternative assembly method
- The input FastQ files must be paired-end reads
- Outputs FASTA file
- Visualisation: Quast output
Gene Prediction
Functional Annotation
Comparative Genomics
Method
Webserver Demo
- Choice One: Running General Pipline
- Choice Two: Running each step separately