https://github.com/nahid18/shasta

De novo assembly from Oxford Nanopore reads on LatchBio
https://github.com/nahid18/shasta

Last synced: about 2 months ago
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De novo assembly from Oxford Nanopore reads on LatchBio

• Host: GitHub
• URL: https://github.com/nahid18/shasta
• Owner: nahid18
• Created: 2022-05-07T15:05:52.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2022-06-04T06:08:18.000Z (over 2 years ago)
• Last Synced: 2024-04-06T01:51:44.492Z (6 months ago)
• Language: Python
• Homepage:
• Size: 180 KB
• Stars: 6
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

• Awesome-LatchBio - latch source code - 2020](https://pubmed.ncbi.nlm.nih.gov/32686750) | [documentation](https://chanzuckerberg.github.io/shasta) (Table of Contents / Genome Assembly)

README

        
# Shasta on [LatchBio](https://latch.bio)

![Interace](./interface.png)

## Quickstart

1. Download test input (`fasta`) and configuration (`conf`) files from [here](https://mega.nz/folder/R1BmiJJI#YFdxk95m13tZJt-6YLDZMA)

2. Create an input directory on [dashboard](https://console.latch.bio/data) and upload your data

3. Add `wf.shasta` to your workspace from [explore](https://console.latch.bio/explore)

4. Go to your [workflows](https://console.latch.bio/workflows) and open `wf.shasta` tool

5. Provide the input directory where `fasta` file is uploaded and also select the `conf` file

6. Launch the workflow

## About Shasta

The goal of Shasta is to rapidly produce accurate assembled sequence using as input DNA reads generated by [Oxford Nanopore](https://nanoporetech.com) flow cells.

## Links

- Configuration Presets: https://github.com/chanzuckerberg/shasta/tree/master/conf

- Source Code: https://github.com/chanzuckerberg/shasta

- Documentation: https://chanzuckerberg.github.io/shasta

- Workflow Code: https://github.com/nahid18/shasta

## How to cite

- Paper: https://www.nature.com/articles/s41587-020-0503-6

- Acknowledgements to external packages: https://chanzuckerberg.github.io/shasta/Acknowledgments.html