This repository contains a set of genome assembly scripts for Team II's genome assembly group.
For general info, see the project's wiki page.
The repository is organized as follows:
.
├── final_pipeline.sh # Final assembly pipeline
├── de_novo.sh # Pipeline just for de novo assembly
├── pre_assebly # A set of pre-assembly (quality control) scripts
├── assembly # A set of scripts for the actual genome assembly
│ ├── de_novo # De novo assembly scripts
│ ├── reference # Reference assembly scripts
├── post_assembly # A set of post-assembly scripts
└
To assemble a genome, run
./final_pipeline -a forward_reads.fastq -b reverse_reads.fastq -o assembly.fasta
To display additional options, run
./final_pipeline -h
The remaining folders contain individual scripts which are not necessarily included in the final pipeline. Some of these scripts might only work on biogenome2018b.biology.gatech.edu server since they rely on specific files present on this server.
No installation is needed, only thing required is to clone the repository and run the final_pipeline.sh script.
However, several dependencies are assumed in the path:
- Trimming
- De Novo
- Skesa (Not open sourced yet)
- SSPACE Standard
- The installation of SSPACE is a little tricky, SSPACE folder needs to be in your path. Please follow the official installation instructions.
- On the server, this means adding
PATH="$PATH:/projects/data/bin/SSPACE"to your .bashrc/profile etc.
- Reference (Currently in development)
A description of each of these tools is available in the project's wiki.