https://github.com/jcaperella29/rna_de_novo_in_bash

https://github.com/jcaperella29/rna_de_novo_in_bash

Last synced: 6 days ago
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• Host: GitHub
• URL: https://github.com/jcaperella29/rna_de_novo_in_bash
• Owner: jcaperella29
• Created: 2025-04-11T17:22:34.000Z (about 1 month ago)
• Default Branch: main
• Last Pushed: 2025-04-11T17:40:50.000Z (about 1 month ago)
• Last Synced: 2025-04-11T18:46:14.262Z (about 1 month ago)
• Language: Shell
• Size: 1.95 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
Description

Performs de novo transcriptome assembly using Trinity with test FASTQ files.

Features

Downloads test read data

Runs Trinity to assemble transcripts

Calculates summary stats including transcript count and N50

Requirements

Trinity (recommended: install via Conda using conda install -c bioconda trinity)

wget, bash, Unix environment

Usage

conda activate trinity_env

bash rna_denovo_assembly.sh