Tools

1. File Tagging & Hierarchy CLI Tool

This command-line utility helps users manage a file hierarchy with relationships between files and directories. Features include:

GitHub Repository: View on GitHub Documentation/Help PDF

Technologies: Bash, MySQL, Linux CLI

2. ThyPredict Pipeline

A bioinformatics CLI tool for thyroid classification, developed using multiple model scripts written by team members. I integrated these scripts and models into a single, seamless pipeline to ensure end-to-end execution.

My Contribution: Integrated all stages into a single command-line pipeline, automated flow, handled error management, and managed GitHub deployment.

Team Contribution: Model development and core script creation by Nimisha (Stage 1 & 2) and Dr. Shweta (Stage 3) under the supervision of Dr. Dinesh Gupta.

GitHub Repository: View on GitHub

Technologies: Python

3. Automated Deployment of Bioinformatics Tools for Workshop at University of Hyderabad

During a genome analysis workshop conducted at the University of Hyderabad, I was responsible for setting up more than 15 bioinformatics tools on over 30 computers. Manual installation on each system would have been time-consuming and error-prone. To overcome this challenge, I designed and developed automated shell scripts that included all necessary package installations and tool dependencies. These scripts were stored on a USB drive and executed with a single-click setup, significantly reducing installation time and ensuring consistency across all systems. This streamlined the workshop setup process, saved hours of repetitive work, and improved reliability.

Skills & Tools Used:: Shell scripting, Linux, Software Automation, Bash, Package Managers (apt/yum), Mamba, USB deployment

Link: View on web

Team Contribution:: All the shell scripts made by myself and Document prepared by: Anwesh Maile

4. AutoQii2 Pipeline

The AutoQii2 Pipeline can be used to analyzing 16S rRNA amplicon based datasets. AutoQii2 is primarily designed for eliminating multi-step analysis involved in analyzing paired-end or single-end reads using QIIME2. AutoQii2 uses popular fastQC, cutadapt and QIIME2 platforms for performing quality check, adapter trimming, ASV feature identification and taxonomic assignments.

My Contribution: Integrated all the steps into a single command-line pipeline.

GitHub Repository: View on GitHub

Technologies: Shell Script

5. Pipeline for Molecular adaptation analysis

The Molecular adaptational analysis were done on the bases of Six indices (referred to as cold-adaptor indicators) namely- frequency of acidic residues; proline residues; aromaticity; aliphacity; grand average of hydrophobicity (GRAVY); and the ratio of arginine (R) and lysine (K) were calculated to estimate cold adaptation at amino-acid level.

My Contribution: Integrated all the steps into a single command-line pipeline.

GitHub Repository: View on GitHub

Technologies: Shell Script