https://github.com/benhg/julia

https://github.com/benhg/julia

Last synced: 19 days ago
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• Host: GitHub
• URL: https://github.com/benhg/julia
• Owner: benhg
• Created: 2020-02-06T19:06:03.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2020-04-23T21:02:00.000Z (over 4 years ago)
• Last Synced: 2024-11-01T22:43:01.256Z (2 months ago)
• Language: Python
• Size: 82 KB
• Stars: 0
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# JULIA

## What is this?

JULIA is a project designed to explain/verify taxon source within a large and complex dataset of possibly contaminated transcriptomes. By "contaminated," here we mean we are not sure exactly from where each of our transcripts came.

## How does it work?

JULIA uses Parsl as an execution environment to carry out alignment and indexing at scale.

## How do I use it?

1. Locate a database of raw reads

2. Create a FASTA file of input transcripts

3. Call JULIA using python and Parsl

4. Extract results with JULIA's data-extraction application.

## What does it do?

Using Alex Dobin's STAR to perform alignment, JULIA indexes and aligns transcripts against a database of raw reads. From there, it is able to generate information about taxon source for each of the transcripts input to it.

## Who wrote it?

Ellen Richards and Ben Glick, expanding on an earlier project by Julia Somers, with advisory support from Greta Binford.

## Who is it named after?

While JULIA is an acronym, it is additionally named after Julia Somers, Lewis & Clark Class of 2019, who designed the project that preceeded it.