Team I Webserver Group: Difference between revisions
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| Line 29: | Line 29: | ||
**Kmer-size | **Kmer-size | ||
**Spades as alternative assembly method | **Spades as alternative assembly method | ||
*The input FastQ files must be | *The input FastQ files must be '''paired-end reads''' | ||
*Outputs as '''FASTA file''' | *Outputs as '''FASTA file''' | ||
*Visualisation: Quast output | *Visualisation: Quast output | ||
Revision as of 03:21, 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 as 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