https://github.com/nextomics/nextsv
https://github.com/nextomics/nextsv
Last synced: about 2 months ago
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- Host: GitHub
- URL: https://github.com/nextomics/nextsv
- Owner: Nextomics
- License: mit
- Created: 2016-12-05T05:30:05.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2024-04-13T19:26:10.000Z (about 1 year ago)
- Last Synced: 2024-04-14T09:52:37.613Z (about 1 year ago)
- Language: C
- Size: 66.4 MB
- Stars: 32
- Watchers: 7
- Forks: 8
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# NextSV3: automated structrual variation detection from long-read sequencing using state-of-the-art tools
NextSV3 uses [Minimap2](https://github.com/lh3/minimap2)/[Winnowmap](https://github.com/marbl/Winnowmap)/[NGMLR](https://github.com/philres/ngmlr) to do read mapping and uses two state-of-the-art SV callers ([Sniffles2](https://github.com/fritzsedlazeck/Sniffles) and [cuteSV2](https://github.com/tjiangHIT/cuteSV)) to do SV calling.
## Table of Contents
- [Table of Contents](#table-of-contents)
- [Installation](#installation)
- [Usage](#usage)
- [Aligners](#aligners)
- [Quick Example](#quick-example)
- [Output files](#output-files)
- [Full Usage](#full-usage)
- [Contact](#contact)
- [Citation](#citation)
- [Included tools](#open-source-software-tools-included-in-this-repository)
## Installation
**Prerequisites**
- Operating System: Linux
- Python 3.8 or later
- [samtools](https://github.com/samtools/samtools) (v1.9 or later)
- [sniffles](https://github.com/fritzsedlazeck/Sniffles) (v2.0.7 or later)
- [cuteSV](https://github.com/tjiangHIT/cuteSV) (v2.0.1 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**
If your OS is Linux, you can acquire precompiled binaries from the [release page](https://github.com/Nextomics/nextsv/releases) with:
```
wget https://github.com/Nextomics/nextsv/releases/download/v3.2.0/NextSV-3.2.0-linux-x86_64.tar.gz
tar xzf NextSV-3.2.0-linux-x86_64.tar.gz
```
If you want to compile from the source code, you need to have the following tools/libraries installed:
- GCC (v7.0 or later)
- GNU make
- CMake
- zlib development files
**You may encounter problems during the compilation process if your operating system is missing any of the above tools/libraries, and we strongly recommend using our pre-compiled binaries if your operating system is Linux.**
To compile NextSV from source:
```
git clone https://github.com/Nextomics/nextsv.git
cd nextsv
make
```
## Usage
### Aligners
The default aligner is `minimap2` as it is faster. But you can use the `-a`/`--aligners` argument to specifiy aligners.
You can use any combination of the following 3 aligners: `minimap2`, `winnowmap`, `ngmlr` (separated by the `+` sign):
```
# use minimap2 only (default)
-a minimap2
# use minimap2 and winnowmap
-a minimap2+winnowmap
# use minimap2, winnowmap and ngmlr
-a minimap2+winnowmap+ngmlr
# use winnowmap and ngmlr
-a winnowmap+ngmlr
# use minimap2 and ngmlr
-a minimap2+ngmlr
# use ngmlr only
-a ngmlr
# use minimap2 only
-a minimap2
```
Please note that if you use more aligners, it would take more time to finish the pipeline.
### Quick Example
```
# PacBio HiFi reads
python path/to/nextsv3.py -a minimap2+winnowmap+ngmlr -i path/to/fastq/folder/ -o ./nextsv_output -s unique_sample_name -r path/to/hg38.fasta -t 8 -p hifi -e nextsv3
# PacBio CLR reads
python path/to/nextsv3.py -a minimap2+winnowmap+ngmlr -i path/to/fastq/folder/ -o ./nextsv_output -s unique_sample_name -r path/to/hg38.fasta -t 8 -p clr -e nextsv3
# Oxford Nanopore reads
python path/to/nextsv3.py -a minimap2+winnowmap+ngmlr -i path/to/fastq/folder/ -o ./nextsv_output -s unique_sample_name -r path/to/hg38.fasta -t 8 -p ont -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.
### Output files
NextSV will generate a `work.sh` in the output directory. Run this `work.sh` and you will get output files. SV calls of sniffles and cuteSV will be generated in the `out_dir/3_SV_calls` folder.
### 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 -a aligners_to_use [-t INT]
[-e conda_env] [--samtools path/to/samtools] [--sniffles path/to/sniffles] [--cuteSV path/to/cuteSV]
[--minimap2 path/to/minimap2] [-v]
nextsv3: an automated pipeline for structrual variation detection from long-read sequencing. Contact: Li Fang([email protected])
options:
-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
-a aligners_to_use, --aligners aligners_to_use
(optional) which aligner(s) to use. Three supported aligners: minimap2, ngmlr, winnowmap. Use "+" to combine multiple
aligners. Examples: minimap2+ngmlr, winnowmap+minimap2, minimap2+ngmlr+winnowmap, minimap2, ngmlr, winnowmap
-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)
--sniffles path/to/sniffles
(optional) path to sniffles (default: using environment default)
--cuteSV path/to/cuteSV
(optional) path to cuteSV (default: using environment default)
--minimap2 path/to/minimap2
this parameter is deprecated as minimap2 is supplied in NextSV now
-v, --version show version number and exit
```
## Contact
If you have any questions/suggestions, please feel free to post it on the [Issue page](https://github.com/Nextomics/nextsv/issues). 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
### Winnowmap
Jain, C., Rhie, A., Hansen, N.F., Koren, S., and Phillippy, A.M. (2022). Long-read mapping to repetitive reference sequences using Winnowmap2. Nat Methods 19, 705-710. https://doi.org/10.1038/s41592-022-01457-8
Jain, C., Rhie, A., Zhang, H., Chu, C., Walenz, B.P., Koren, S., and Phillippy, A.M. (2020). Weighted minimizer sampling improves long read mapping. Bioinformatics 36, i111-i118. https://doi.org/10.1093/bioinformatics/btaa435
### NGMLR and 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
Smolka, M., Paulin, L.F., Grochowski, C.M., Mahmoud, M., Behera, S., Gandhi, M., Hong, K., Pehlivan, D., Scholz, S.W., Carvalho, C.M.B., et al. (2022). Comprehensive Structural Variant Detection: From Mosaic to Population-Level. bioRxiv. https://doi.org/10.1101/2022.04.04.487055
### 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
Cao, S., Jiang, T., Liu, Y., Liu, S., and Wang, Y. (2022). Re-genotyping structural variants through an accurate force-calling method. bioRxiv. https://doi.org/10.1101/2022.04.04.487055
### 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
## Open source software tools included in this repository
To provide consistent output and better user experience, we included some open source software tools.
**LongReadQC** https://github.com/fangli80/longreadqc
**Seqtk**
https://github.com/lh3/seqtk
**Minimap2**
https://github.com/lh3/minimap2
**NGMLR**
https://github.com/philres/ngmlr
**pigz**
https://github.com/madler/pigz
**Winnowmap**
https://github.com/marbl/Winnowmap