nvk747 / arima-sv-pipeline

Arima SV Pipeline for Mapping, SV Detection and QC

To order Arima kits, please visit our website: https://arimagenomics.com/

Getting Started

We provide both Docker and Singularity container implementations of the pipeline for users to run Arima SV pipeline out of the box. You can mount the necessary input and output locations and run Arima SV pipeline in two ways.

For advanced users, we also provide a non-containerized version of the pipeline in this repository. You will need to install all the tools and dependencies yourself.

Using Docker image

Please refer to the manual on Arima's DockerHub: https://hub.docker.com/repository/docker/arimaxiang/arima_sv

Using Singularity image

• How to run Singularity on HPC when it is pre-installed

module load singularity

• How to install on Ubuntu systems. Note: not needed for use on TSCC, see above. Source: https://apptainer.org/user-docs/master/quick_start.html

sudo apt-get update && sudo apt-get install -y build-essential libssl-dev uuid-dev libgpgme11-dev squashfs-tools libseccomp-dev wget pkg-config git cryptsetup

• Install Go Download Go installer for Linux

wget https://go.dev/dl/go1.17.6.linux-amd64.tar.gz

• Remove any previous installation of Go

sudo rm -rf /usr/local/go

• Extract Go and put it in the directory '/usr/local'

sudo tar -C /usr/local -xzf go1.17.6.linux-amd64.tar.gz

• Add Go to the $PATH variable

export PATH=$PATH:/usr/local/go/bin
echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc && source ~/.bashrc

• Verify Go installation

go version  # Expected: 'go version go1.17.6 linux/amd64'

• Create a variable with the version of Singularity to be downloaded

export VERSION=3.8.5  # Adjust this as necessary

• Download the Singularity source code

wget https://github.com/hpcng/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz

• Extract the Singularity code

tar -xzf singularity-${VERSION}.tar.gz

• Change directory into the Singularity directory

cd singularity-${VERSION}

• Compile the Singularity source code

./mconfig
make -C builddir
sudo make -C builddir install

• Verify Singularity Installation

singularity version  # '3.8.5'

• Download Arima's Singularity container for SV pipeline

wget ftp://ftp-arimagenomics.sdsc.edu/pub/singularity/Arima-SV-Pipeline-singularity-v1.sif

• Run the pipeline with Singularity (Adjust this as necessary)

singularity exec -B YOUR_HOST_OUTPUT_DIR:/FFPE/mydata/ Arima-SV-Pipeline-singularity-v1.sif bash /FFPE/Arima-SV-Pipeline-v1.sh -W 1 -B 1 -J 1 -H 0 -a /root/anaconda3/bin/bowtie2 -b /usr/local/bin/ -w /FFPE/HiCUP-0.8.0/ -j /FFPE/juicer-1.6/ -r /FFPE/Arima_files/reference/hg38/hg38.fa -s /FFPE/Arima_files/Juicer/hg38.chrom.sizes -c /FFPE/Arima_files/Juicer/hg38_GATC_GANTC.txt -x /FFPE/Arima_files/reference/hg38/hg38 -d /FFPE/Arima_files/HiCUP/Digest_hg38_Arima.txt -I /FFPE/test_data/fastq/JB_3_5M_R1.fastq.gz,/FFPE/test_data/fastq/JB_3_5M_R2.fastq.gz -o /FFPE/mydata/ -p JB_3_5M -e /FFPE/Arima_files/hic_breakfinder/intra_expect_100kb.hg38.txt -E /FFPE/Arima_files/hic_breakfinder/inter_expect_1Mb.hg38.txt -t 12 &> log.txt

Usage (Command line options)

Arima-SV-Pipeline-v1.sh [-W run_hicup] [-B run_hic_breakfinder] [-J run_juicer] [-H run_hiccups] [-r reference_file] [-s chrom_sizes_file] [-c cut_site_file] [-a bowtie2] [-x bowtie2_index_basename] [-d digest] [-w hicup_dir] [-b hic_breakfinder_dir] [-j juicer_dir] [-I FASTQ_string] [-o out_dir] [-p output_prefix] [-e exp_file_intra] [-E exp_file_inter] [-t threads] [-v] [-h]

• [-W run_hicup]: "1" (default) to run HiCUP pipeline, "0" to skip. If skipping, HiCUP_summary_report_*.txt and R1_2.hicup.bam need to be in the HiCUP output folder.
• [-B run_hic_breakfinder]: "1" (default) to run hic_breakfinder, "0" to skip
• [-J run_juicer]: "1" (default) to run Juicer, "0" to skip
• [-H run_hiccups]: "1" to run HiCCUPS, "0" (default) to skip
• [-r reference_file]: reference FASTA file
• [-s chrom_sizes_file]: chrom.sizes file generated from the reference file
• [-c cut_site_file]: cut site file used by Juicer pipeline
• [-a bowtie2]: bowtie2 tool location
• [-x bowtie2_index_basename]: bowtie2 index file prefix
• [-d digest]: genome digest file produced by hicup_digester
• [-w hicup_dir]: directory of the HiCUP tool
• [-b hic_breakfinder_dir]: directory of the hic_breakfinder tool
• [-j juicer_dir]: directory of the Juicer tool
• [-I FASTQ_string]: a pair of FASTQ files separated by "," (no space is allowed)
• [-o out_dir]: output directory
• [-p output_prefix]: output file prefix (filename only, not including the path)
• [-e exp_file_intra]: intra-chromosomal background model file for normalization
• [-E exp_file_inter]: inter-chromosomal background model file for normalization
• [-t threads]: number of threads to run HiCUP and Juicer
• [-v]: print version number and exit
• [-h]: print this help and exit

Example

bash /FFPE/Arima-SV-Pipeline-v1.sh -W 1 -B 1 -J 1 -H 0 -a /root/anaconda3/bin/bowtie2 -b /usr/local/bin/ -w /FFPE/HiCUP-0.8.0/ -j /FFPE/juicer-1.6/ -r /FFPE/Arima_files/reference/hg38/hg38.fa -s /FFPE/Arima_files/Juicer/hg38.chrom.sizes -c /FFPE/Arima_files/Juicer/hg38_GATC_GANTC.txt -x /FFPE/Arima_files/reference/hg38/hg38 -d /FFPE/Arima_files/HiCUP/Digest_hg38_Arima.txt -I /FFPE/test_data/fastq/JB_3_5M_R1.fastq.gz,/FFPE/test_data/fastq/JB_3_5M_R2.fastq.gz -o /FFPE/test_data/test_output_docker/ -p JB_3_5M -e /FFPE/Arima_files/hic_breakfinder/intra_expect_100kb.hg38.txt -E /FFPE/Arima_files/hic_breakfinder/inter_expect_1Mb.hg38.txt -t 12 &> /FFPE/test_data/test_output_docker/log.txt

Pipeline Outputs

The Arima SV pipeline Bioinformatics User Guide walks through an example of how to run the Arima SV pipeline using the provided test data and provides additional information on the output files. The Arima SV pipeline generates multiple files. Main output files are:

Arima Shallow Sequencing QC

[output_directory]/[output_prefix]_Arima_QC_shallow.txt

Contents: This file includes QC metrics for assessing the shallow sequencing data for each CHiC library.

• Break down of the number of read pairs
• The target sequencing depth for deep sequencing
• The percentage of long-range cis interactions that overlap the probe regions

Arima Deep Sequencing QC

[output_directory]/[output_prefix]_Arima_QC_deep.txt

Contents: This file includes QC metrics for assessing the deep sequencing data for each CHiC library.

• Break down of the number of read pairs
• The number of loops called
• The percentage of long-range cis interactions that overlap the probe regions

SV file in .bedpe format from hic_breakfinder

[output_directory]/hic_breakfinder/[output_prefix].breaks.bedpe

Arima HiC heatmap for visualization using Juicebox

[output_directory]/juicer/aligned/inter_30.hic

Arima Pipeline Version

1.0

Support

For Arima customer support, please contact [email protected]

Acknowledgments

Authors of HiCUP: https://www.bioinformatics.babraham.ac.uk/projects/hicup/

• Wingett S, et al. (2015) HiCUP: pipeline for mapping and processing Hi-C data F1000Research, 4:1310 (doi: 10.12688/f1000research.7334.1)

Authors of HiC_breakfinder: https://github.com/dixonlab/hic_breakfinder

• Dixon, J. R., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V. T., ... & Yue, F. (2018). Integrative detection and analysis of structural variation in cancer genomes. Nature genetics, 50(10), 1388-1398.

Authors of Juicer: https://github.com/aidenlab/juicer

• Neva C. Durand, Muhammad S. Shamim, Ido Machol, Suhas S. P. Rao, Miriam H. Huntley, Eric S. Lander, and Erez Lieberman Aiden. "Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments." Cell Systems 3(1), 2016.