CtGAP - Chlamydia trachomatis Genome Assembly Pipeline

Install

1. git clone this repo:

git clone https://github.com/ammaraziz/ctgap

2. Install miniconda or preferrably mamba

   • https://mamba.readthedocs.io/en/latest/installation.html
   • https://docs.conda.io/projects/miniconda/en/latest/

3. Install snakemake:

   mamba install -c bioconda snakemake 

Manually install rust/scrubby

mamba install -c conda-forge rust
cargo install scrubby

4. Download the human genome, rename to resources/grch38.fasta

   • From NCBI

5. Download one of the kraken dbs with bacterial genomes, rename to resources/standardDB:

   • https://benlangmead.github.io/aws-indexes/k2

6. Done - The pipeline will handle the dependencies internally.

Usage

1. Create a folder ctgap/input/

2. Add your fastq.gz files in ctgap/input/.

   • Ensure they're named as follows: {sample_name}_{direction}.fastq.gz.
     • eg SRR12345_R1.fastq.gz and SRR12345_R2.fastq.gz.

3. In ctgap/ folder run the pipeline:

   snakemake -j 8 --use-conda -k

• -j 8 specifies the number of threads to use in total.
• --use-conda tells snakemake to install the dependencies.
• -k tells snakemake to keep going if a sample fails.

Dependencies

• Snakemake
• Spades
• Shovill
• Bowtie2
• Samtools
• fastp
• bbmap (bbnorm)
• kraken2
• multiqc
• blast+

Output

TBA

Cite

Pipeline is created by Shola Olagoke with assistance from Ammar Aziz.