seqoccinlr

This Snakemake pipeline starts from a set of nanopore reads and an associated genome, simulate reads, map them to the genome with 2 different tools (minimap2 and ngmlr) and compute various statistics about the correctness of the mapping

Dependencies

• snakemake-minimal =5.2.4
• python =3.6.3
• samtools =1.9
• pysam =0.15.0
• nanostat =1.1.0
• seqtk =1.3
• minimap2 =2.11
• nanosim =2.2.0
• ngmlr =0.2.7
• drmaa =0.7.6

Usage

Step 1: Install workflow

To use this workflow, first download it:

git clone https://github.com/SeqOccin-SV/seqoccinlr.git

This pipeline needs all the tools and versions indicated in the file environment.yaml. An easy way to achieve this is to create a conda environment. For this you need conda (or Miniconda3-4.4.10) and to execute the following commands:

cd seqoccinlr

conda env create --name [yourname] --file environment.yaml

conda activate [yourname]

Step 2: Configure workflow

Configure the workflow according to your needs via editing the file config.yaml.

Step 3: Execute workflow

Test your configuration by performing a dry-run via

snakemake -n

Execute the workflow locally via

snakemake --cores $N

using $N cores or run it in a cluster environment via

snakemake --cluster qsub --jobs 100

or

snakemake --drmaa --jobs 100