NextSV2: an automated pipeline for structrual variation detection from long-read sequencing.

NextSV2 uses two aligners (Minimap2 and NGMLR) to do read mapping and uses Sniffles to do SV calling.

Installation

Prerequisites: sniffles, samtools (version 1.3 or later), gcc/g++(>=4.8.2), python 2.7

Installation:

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

Usage

python nextsv2.py <config> <sample_name> <input_fastq_folder>

sample_name is a unique name or id for the input sample.

input_fastq_folder is the folder that contains all input fastq files. NextSV2 will search the folder and all fastq files (.fastq or .fq) found in this folder will be treated as input files.

A template config file can be found in example.config.

Please use full paths in the config file and input list file.

Output files

Please go to the output directory. There will be a work.sh. Please run the work.sh locally or submit it to the cluster. The output VCF files is in the sniffles_calls directory.

Contact

For questions/bugs/issues, please post on GitHub. In general, please do NOT send questions to our email. Your question may be very likely to help other users.

Citation

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

More information

• NextSV Homepage

Copyright

Copyright of NextSV

NextSV is freely available for academic use. It is provided without warranty of any kind, including but not limited to the warranties of merchantability, fitness for a particular purpose and non-infringement. No liability for the software usage is assumed.

For commercial use please contact Grandomics Biosciences ([email protected]) for licensing options.

Redistribution is allowed. Modification is allowed. Redistribution of modified version is not allowed, but users can submit a push request to github, and after reviewing the modification, we may accept it in the master branch.