About

Pipeline gets assembly in fasta format, and reads in fq format as default (see Required settings section below). As an output it generates ... (pipeline is in progress).

All general results you can find in data_output folder.

All additional information can also be found in readme files incide required directories.

Configure Pipeline

git clone https://github.com/rutaolta/reseqpipe.git

cd <pipeline_working_dir>

It is recommended to create a fresh conda environment using mamba or conda.

mamba env create --name reseqpipe --file ./environment.yaml
# or:
# conda env create --name reseqpipe --file ./environment.yaml

Activate conda environment with snakemake:

conda activate reseqpipe

Run

snakemake --cores 32 --configfile config/config.yaml --forceall --use-conda --profile profile/slurm/ --printshellcmds --latency-wait 60

Required settings

Extensions of assembly and reads can be changed in config/config.yaml in "Extensions" section:

- `assemblies_ext: "your desired extension"`

- `reads_ext: "your desired extension"`

The name of file with reference assembly should be defined in config/default.yaml in "Parameters" section:

- `reads: ["name of your desired reads"]`

Actually this is the common part of filenames containing forward and reverse reads. Filename should be without extensions. For example, if desired reads are cerevisiae_1.fq.gz and cerevisiae_2.fq.gz then the setting would be like reads: ["cerevisiae"].

Suffix of filename with foward read should be "_1" and with reverse "_2". For example, cerevisiae_1.fq.gz

- `assembly: ["name of your desired assembly"]`

Actually this is the name of files containing assembly. Filename should be without extensions. For example, if desired assembly is s.cerevisiae.fasta.gz then the setting would be like assembly: "s.cerevisiae".

The mapping quality for mosdepth can be changed in config/default.yaml in "Parameters" section:

- `min_mapping_quality: your_desired_quality_integer` (20 as default)