https://github.com/mobinasri/hpp-assembly

https://github.com/mobinasri/hpp-assembly

Last synced: 1 day ago
JSON representation

• Host: GitHub
• URL: https://github.com/mobinasri/hpp-assembly
• Owner: mobinasri
• Created: 2020-07-22T22:43:18.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2020-12-13T01:39:58.000Z (about 4 years ago)
• Last Synced: 2024-11-10T14:54:28.818Z (about 2 months ago)
• Language: wdl
• Size: 11.4 MB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
## Human Pan-Genome Project and Hifiasm 

This repository contains the workflow, Dockerfile and some test json files to run [hifiasm](https://github.com/chhylp123/hifiasm), a haplotype-resolved de novo assembler for PacBio Hifi reads. The workflow is going to be used in generating the inital assemblies of the samples sequenced by [Human Pan-Genome Project](https://humanpangenome.org/).

## Dependencies to run locally

### Cromwell

https://cromwell.readthedocs.io/en/stable/tutorials/FiveMinuteIntro/

### Docker

https://docs.docker.com/engine/install/

## Instructions to run locally

After installing Cromwell and Docker make sure to have the child and parents reads set (i.e in fastq , fastq.gz or bam format) available locally. Then you have to modify inputs.json based on your instance type and the name of input files. Here we provide read sets for chromosome 20 and instructions to run this as a test.

```bash

git clone https://github.com/masri2019/hpp-assembly/

mkdir data

cd data

wget https://storage.googleapis.com/hifiasm/HG003.GRCh38.2x250.chrom20.fastq.gz

wget https://storage.googleapis.com/hifiasm/HG004.GRCh38.2x250.chrom20.fastq.gz

wget https://storage.googleapis.com/hifiasm/pFDA_HG002_CCS_35X_2_GRCh38_no_alt.chrom20.fastq.gz

cd ../

java -jar ${CROMWELL_JAR_PATH} run assembly.wdl --inputs inputs.json

```