shahcompbio/nanogenome

Introduction

shahcompbio/nanogenome is a bioinformatics pipeline for comprehensive analysis of long-read DNA sequencing data. The pipeline performs variant calling, phasing, structural variant (SV) detection, copy number aberration (CNA) analysis, and gene annotation from Oxford Nanopore Technologies (ONT) sequencing data. It supports both somatic (tumor-normal) and germline analysis workflows with ensemble calling approaches for improved accuracy.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

Pipeline summary

1. Variant calling and phasing (Clair3, LongPhase)
2. BAM haplotagging (WhatsHap)
3. Somatic structural variant calling with ensemble approach
   • Individual callers: SEVERUS, SAVANA, NanoMonSV
   • Consensus calling: MINDA
4. Germline structural variant calling (optional)
   • Individual callers: SEVERUS, Sniffles, CuteSV, LongcallD
   • Consensus calling: MINDA
5. Haplotype-resolved copy number analysis (Wakhan, SAVANA)
6. SV and CNA annotation (BioMart, OncoKB)
7. Visualization of SVs and CNAs (Circos for somatic, karyoplot for germline)
8. Present QC for all workflow stages (MultiQC)

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,condition,bam,bai,vcf,tbi
SAMPLE_TUMOR,tumor,/path/to/tumor.bam,/path/to/tumor.bam.bai,,
SAMPLE_NORMAL,normal,/path/to/normal.bam,/path/to/normal.bam.bai,,

Each row represents a sample with the following columns:

• sample: Sample identifier (must be the same for tumor-normal pairs)
• condition: Either tumor or normal
• bam: Full path to aligned BAM file
• bai: Full path to BAM index file
• vcf: (Optional) Path to pre-phased VCF file (required if --skip_phasing is used)
• tbi: (Optional) Path to VCF index file

Now, you can run the pipeline using:

nextflow run shahcompbio/nanogenome \
   -profile docker \
   --input samplesheet.csv \
   --outdir <OUTDIR> \
   --fasta <REFERENCE_FASTA> \
   --fai <REFERENCE_FAI>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

shahcompbio/nanogenome was originally written by Asher Preska Steinberg.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.