Inspectro is a bioinformatics pipeline that characterizes long-range interaction profiles in Hi-C maps by spectral decomposition. The pipeline is built using Nextflow, a workflow tool that enables easy installation and reproducibility of the pipeline through Docker containers.

This pipeline (v1.2) supports S3 files for bigwig/bigbed tracks.

Note: Local files are not currently supported.

Future update: Adding iGenomes, which will provide the option to use your own fasta file or one provided by iGenomes for the genome of your choice.

1. Install Nextflow (>=21.10.3)

2. Install Docker to implement environment for pipeline reproducibility. Build the Docker image: docker build -t open2c/inspectrov1.2:latest ./docker

3. Place supplementary tab-delimited bigwig file with a header in data/track_metadata.tsv to include in graphical outputs. The following columns must be included:

• Name: a display name
• ID: a unique identifier to use in the database (can be the same as Name)
• FileFormat: must be the string bigWig
• Path: a local absolute path to the file

4. Add supplementary bigwig track names, sample name and genome assembly name to the params.yml file.

5. Finally, you can run the pipeline using:

nextflow run main.nf \
    --config params.yml \
    --genome <FASTA_file> \
    --meta track_metadata.tsv \
    --outdir <OUTDIR> \
    --blacklist <blacklist_file> \
    --mcool <mcool_file> \
    -profile docker

Tarishi Pathak, Aleksandra Galitsyna, George Spracklin, Nezar Abdennur

@article{spracklin2022diverse,
  title={Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers},
  author={Spracklin, George and Abdennur, Nezar and Imakaev, Maxim and Chowdhury, Neil and Pradhan, Sriharsa and Mirny, Leonid A and Dekker, Job},
  journal={Nature Structural \& Molecular Biology},
  pages={1--14},
  year={2022},
  publisher={Nature Publishing Group}
}