mobile_elements

Nextflow workflow for the detection of mobile elements from NGS data

Installation

Clone the git repository:

git clone https://github.com/Timniem/mobile_elements/

Get Melt from: https://melt.igs.umaryland.edu/downloads.php and unpack the tarball in ./mobile_elements/resources/melt:

tar -xvzf MELTvx.x.x.tar.gz

Create transposon file lists from ./mobile_elements/resources/melt/MELTvx.x.x/me_refs (local paths) for the genome build you want to use and add them to ./mobile_elements/resources/melt :

# They should be plain txt files with the local paths per line.
# Example:
"
path/to/SVA_MELT.zip
path/to/LINE1_MELT.zip
...
"

Add the SylabsCloud to the remotes on Apptainer:

apptainer remote add --no-login SylabsCloud cloud.sylabs.io
apptainer remote use SylabsCloud

If not already configured:

export APPTAINER_CACHEDIR=/path/to/your/tmp

Get the Singularity images and add them to ./mobile_elements/containers/ :

• SCRAMble: library://timniem/misc/scramble
• Melt: library://timniem/misc/melt

apptainer pull --dir 'path/to/cache/dir' container_name.sif library://timniem/container_image_path

Usage

• Create a tab separated sample sheet consisting of the following sections:

sampleID	bamFile
example_1	example_1.bam
example_2	example_2.bam

• ajust the nextflow.config to your needs (TIP: Or create a bash script for every new run, adjusting only the necessary parameters)

# In the mobile_elements folder:
nextflow run main.nf

Adjustable parameters

Parameter	Description	default	required
samplesheet	Tab-separated file with samplename and BAM path	None	Yes
reference_genome	Reference genome used for the alignment of the BAM	None	Yes
genomeBuild	Genome build version used: hg19 or hg38)	'hg38'	Yes
output	Output folder in which the .VCF with MEI calls will be stored	None	Yes