layout: page

Link to the repository

First follow the instructions here:

Step by step guide on how to use my pipelines
Click here for an introduction to Snakemake

ABOUT

This is a pipeline to map short reads to a reference assembly. It outputs the mapped reads, a qualimap report and does variant calling.

Tools used:

• Bwamem2 - mapping

• Samtools - processing

• Qualimap - mapping summary

• Freebayes - variant calling

| | |:--:| | Pipeline workflow |

Edit config.yaml with the paths to your files

OUTDIR: /path/to/output
READS_DIR: /path/to/reads/ # don't add the reads files, just the directory where they are
ASSEMBLY: /path/to/assembly
PREFIX: <output name>

• OUTDIR - directory where snakemake will run and where the results will be written to

• READS_DIR - path to the directory that contains the reads

• ASSEMBLY - path to the assembly file

• PREFIX - prefix for the final mapped reads file

If you want the results to be written to this directory (not to a new directory), and comment out OUTDIR: /path/to/output in the config file

For the mapping step you should have one _1 fastq file and one _2 fastq file in READS_DIR . If you have several _1 and _2 fastq files from the same sample, you can combine them so you have one file for all _1 reads and one for all the _2 reads. This can be done by concatenating them using cat , if the original files are not compressed ( fastq or fq extension), or zcat if the original files are compressed ( fastq.gz or fq.gz extension). Example where your files are in the same directory and are compressed:

zcat *_1.fastq.gz > <new file name>_1.fastq.gz
zcat *_2.fastq.gz > <new file name>_2.fastq.gz

RESULTS

• dated file with an overview of the files used to run the pipeline (for documentation purposes)

• sorted_reads directory with the file containing the mapped reads

• results directory containing the qualimap results

• variant_calling directory containing the variant calling VCF file and file with VCF statistics