slavseq_rf

Analysis pipeline for human LINE-1 targeted sequencing data obtained with the SLAV-Seq protocol.

Publication

https://doi.org/10.1038/nn.4388

Prerequisites

• rf
• pyslavseq
• snakemake
• cutadapt
• bwa-mem
• tabix
• python
• perl

How to use

This pipeline uses rf (https://github.com/apuapaquola/rf) to manage workflow.

• clone the repository
• move the pipeline directory to a suitable location
• edit _h/run scripts or set the BASE_DIR to /path/to/pipeline
• go to pipeline/genome and rf run -r . to download and index hg19
• add your fastq files
• go to pipeline/genome and rf run -r .