https://github.com/gregor-mendel-institute/isoseq3

https://github.com/gregor-mendel-institute/isoseq3

Last synced: 7 days ago
JSON representation

• Host: GitHub
• URL: https://github.com/gregor-mendel-institute/isoseq3
• Owner: Gregor-Mendel-Institute
• Created: 2018-07-30T19:04:27.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2019-03-08T16:21:09.000Z (over 5 years ago)
• Last Synced: 2024-03-26T21:06:39.289Z (8 months ago)
• Language: Nextflow
• Size: 63.5 KB
• Stars: 3
• Watchers: 7
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# isoseq3

This is a [nextflow](https://github.com/nextflow-io/nextflow) implementation of [Pacific Biosciences IsoSeq3.1 pipeline](https://github.com/PacificBiosciences/IsoSeq3/blob/master/README_v3.1.md).

## Setup

### Requirements

This pipeline requires [anaconda](https://anaconda.org/). The required dependencies will then be installed by nextflow into a conda virtual environment

### Configuration

The current pipeline is designed to run on the Mendel cluster of the [GMI Vienna](https://www.gmi.oeaw.ac.at/). To make it run for your group edit the `projectName` & `fasta` parameters in the the mendel.config file to fit to your group project and needs. To make it run on another infrastructure simply add a new nextflow config file in the conf folder and source via the nextflow.config file. See [here](https://www.nextflow.io/docs/latest/config.html) for more information. 

## Workflow of the pipeline

1. circular consensus calling

2. primer removal

3. refine reads

4. merge samples (optional)

3. cluster reads 

4. polish reads

5. align transcripts (optional)

## Run the pipeline

To run the pipeline simply run e.g:

```bash

nextflow run_isoseq3.nf --input "/lustre/scratch/users/falko.hofmann/isoseq/samples/*/" --output "/lustre/scratch/users/falko.hofmann/isoseq/results/*/