snakemake_pipelines/bowtie2_markdup/README.md

In navinlabcode/copykit: CopyKit

Alignment and Mark Duplicates

This snakemake pipeline performs alignment and removal of PCR duplicates from a fastq file.

Output

A sorted .bam file for each aligned sampled with duplicates marked.

Installation

Make sure to install and properly run snakemake, clone this repository and run the snakefile.

Usage

All .fastq files must be inside a folder called fastq. After that run:

snakemake --snakefile /PATH/TO/SNAKEFILE/bowtie_markdup.smk --cores 60 

For paired-end reads, run:

snakemake --snakefile /PATH/TO/SNAKEFILE/bowtie2_markdup_pairend.smk --cores 60 

Dependencies

• snakemake
• sambamba

Pipeline steps

This pipelines uses bowtie2 to align reads to hg38 and sambamba to mark duplicates.

navinlabcode/copykit documentation built on Oct. 16, 2024, 2:55 p.m.