fangli80/nextsv

NextSV3: automated structrual variation detection from long-read sequencing using state-of-the-art tools.

NextSV3 uses Minimap2 to do read mapping and uses two state-of-the-art SV callers (Sniffles and cuteSV) to do SV calling.

Installation

Prerequisites

• Python 3.8 or later
• samtools (v1.9 or later)
• minimap2 (v2.22 or later)
• sniffles (v2.0.7 or later)
• cuteSV (v2.0.1 or later)
• GCC (v4.8.2 or later)

Conda environment is not required but we highly recommend you install the prerequisites in a new conda environment to avoid potential dependency issues.

conda create -n nextsv3 python=3.8
conda activate nextsv3
pip install "setuptools<58.0"
pip install sniffles
pip install cuteSV

Installation of NextSV3

git clone --recursive   https://github.com/Nextomics/nextsv.git
cd nextsv/
sh build.sh

Usage

Quick Example

# Oxford Nanopore reads
python path/to/nextsv3.py  -i path/to/fastq/folder/ -o ./nextsv_output -s unique_sample_name -r path/to/hg38.fasta -t 8 -p ont -e nextsv3

# PacBio CLR reads
python path/to/nextsv3.py  -i path/to/fastq/folder/ -o ./nextsv_output -s unique_sample_name -r path/to/hg38.fasta -t 8 -p clr -e nextsv3

# PacBio HiFi reads
python path/to/nextsv3.py  -i path/to/fastq/folder/ -o ./nextsv_output -s unique_sample_name -r path/to/hg38.fasta -t 8 -p hifi -e nextsv3

Memory consumption of the pipeline depends on number of threads and the size of the reference genome. For human genomes (3Gb), we recommend 4GB memory per thread.

Full Usage

usage: nextsv3.py [-h] -i path/to/input_dir -o path/to/output_dir -s sample_name -r ref.fasta -p sequencing_platform [-t INT] [-e conda_env] [--samtools path/to/samtools] [--minimap2 path/to/minimap2]
                  [--sniffles path/to/sniffles] [--cuteSV path/to/cuteSV] [-v]

nextsv3: an automated pipeline for structrual variation detection from long-read sequencing. Contact: Li Fang([email protected])

optional arguments:
  -h, --help            show this help message and exit
  -i path/to/input_dir, --in_dir path/to/input_dir
                        (required) path to input FASTQ/FASTA directory (all fastq/fasta files in this directory will be used as input files)
  -o path/to/output_dir, --out_dir path/to/output_dir
                        (required) path to output fastq directory
  -s sample_name, --sample_name sample_name
                        (required) a unique name or id for the input sample
  -r ref.fasta, --ref_fasta ref.fasta
                        (required) path to reference genome sequence in FASTA format
  -p sequencing_platform, --platform sequencing_platform
                        (required) sequencing platform. Three valid values: ont/clr/hifi ont: oxford nanopore; clr: PacBio CLR; hifi: PacBio HiFi/CCS
  -t INT, --threads INT
                        (optional) number of threads (default: 4)
  -e conda_env, --conda_env conda_env
                        (optional) conda environment name (default: NULL)
  --samtools path/to/samtools
                        (optional) path to samtools (default: using environment default)
  --minimap2 path/to/minimap2
                        (optional) path to minimap2 (default: using environment default)
  --sniffles path/to/sniffles
                        (optional) path to sniffles (default: using environment default)
  --cuteSV path/to/cuteSV
                        (optional) path to cuteSV (default: using environment default)
  -v, --version         show program's version number and exit

Output files

SV calls of sniffles and cuteSV will be generated in the out_dir/3_SV_calls folder.

Contact

If you have any questions/suggestions, please feel free to post it on the Issue page. You may also email me at [email protected].

Citation

NextSV

Fang, L., Hu, J., Wang, D. et al. NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data. BMC Bioinformatics 19, 180 (2018). https://doi.org/10.1186/s12859-018-2207-1

Minimap2

Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100 (2018). https://doi.org/10.1093/bioinformatics/bty191

Sniffles

Sedlazeck, F.J., Rescheneder, P., Smolka, M. et al. Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods 15, 461–468 (2018). https://doi.org/10.1038/s41592-018-0001-7

CuteSV

Jiang, T., Liu, Y., Jiang, Y. et al. Long-read-based human genomic structural variation detection with cuteSV. Genome Biol 21, 189 (2020). https://doi.org/10.1186/s13059-020-02107-y

Samtools

Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li, Twelve years of SAMtools and BCFtools, GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008