git clone
this repo:
git clone https://github.com/ammaraziz/ctgap
-
Install
miniconda
or preferrablymamba
-
Install
snakemake
:
mamba install -c bioconda snakemake
Manually install rust/scrubby
mamba install -c conda-forge rust
cargo install scrubby
-
Download the human genome, rename to
resources/grch38.fasta
-
Download one of the kraken dbs with bacterial genomes, rename to
resources/standardDB
: -
Done - The pipeline will handle the dependencies internally.
-
Create a folder
ctgap/input/
-
Add your fastq.gz files in
ctgap/input/
.- Ensure they're named as follows:
{sample_name}_{direction}.fastq.gz
.- eg
SRR12345_R1.fastq.gz
andSRR12345_R2.fastq.gz
.
- eg
- Ensure they're named as follows:
-
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.
- Snakemake
- Spades
- Shovill
- Bowtie2
- Samtools
- fastp
- bbmap (bbnorm)
- kraken2
- multiqc
- blast+
TBA
Pipeline is created by Shola Olagoke with assistance from Ammar Aziz.