Team I Webserver Group: Difference between revisions

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==Functionalities==
==Functionalities==
===De Novo Genome Assembly===
===De Novo Genome Assembly===
De novo sequencing was used in our pipeline because no reference sequence is needed in this case. Sequence reads are assembled as contigs, and the coverage quality of de novo sequence data depends on the size and continuity of the contigs. We used Skesa for de novo genome assembly. This tool is currently unpublished.
===Species & Strain Typing===
===Species & Strain Typing===
===Genome Database===
===Genome Database===
We created a curated list of genes that are included in the 258 Klebsiella genomes​ we were given, performed a literature review to find genes that may indicate colistin resistance​, and built a gene panel to help us find phenotypic indicators in our assembled genomes. We will be using a MySQL database that will show 0 (absent) or 1 (present) for both antibiotic resistance genes and virulence factor genes.
We created a curated list of genes that are included in the 258 Klebsiella genomes​ we were given, performed a literature review to find genes that may indicate colistin resistance​, and built a gene panel to help us find phenotypic indicators in our assembled genomes. We will be using a MySQL database that will show 0 (absent) or 1 (present) for both antibiotic resistance genes and virulence factor genes.

Revision as of 11:13, 23 April 2018

Web Server

Team

Dongjo Ban, Genevieve Brandt, Yuntian He, Ryan Place, Nirav Shah, Casey Smith, Mohit Thakur, Stephen Wist

Introduction

Background

The goal of our predictive webserver is to process biological data​ and output the results of the analysis in a user-friendly format. We will provide information about an input sample's antibiotic resistance and other biological traits such as genus, species, and strain.

Goals

  • Assemble input reads​
  • Analyze assemblies​
  • Visualize results​
  • Implement a way for results to be downloaded

Technologies Used

PHP was used because it is a universal web language that has numerous useful libraries and is easy to integrate with HTML. This was used with Laravel to allow for rapid application development.

Functionalities

De Novo Genome Assembly

De novo sequencing was used in our pipeline because no reference sequence is needed in this case. Sequence reads are assembled as contigs, and the coverage quality of de novo sequence data depends on the size and continuity of the contigs. We used Skesa for de novo genome assembly. This tool is currently unpublished.

Species & Strain Typing

Genome Database

We created a curated list of genes that are included in the 258 Klebsiella genomes​ we were given, performed a literature review to find genes that may indicate colistin resistance​, and built a gene panel to help us find phenotypic indicators in our assembled genomes. We will be using a MySQL database that will show 0 (absent) or 1 (present) for both antibiotic resistance genes and virulence factor genes.