cuteSV

Getting Start

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Installation

$ pip install cuteSV
or
$ conda install -c bioconda cutesv
or 
$ git clone https://github.com/tjiangHIT/cuteSV.git && cd cuteSV/ && pip install .

Introduction

Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV signatures implied by the noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and it employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmark on real PacBio and ONT datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.

The benchmark results of cuteSV on the HG002 human sample are below:

BTW, we used Truvari to calculate the recall, precision, and f-measure.

Dependence

1. python3
2. pysam
3. Biopython
4. cigar
5. numpy

Usage

cuteSV <sorted.bam> <output.vcf> <work_dir>

Suggestions

> For PacBio CLR data:
	--max_cluster_bias_INS		100
	--diff_ratio_merging_INS	0.2
	--diff_ratio_filtering_INS	0.6
	--diff_ratio_filtering_DEL	0.7
> For PacBio CCS(HIFI) data:
	--max_cluster_bias_INS		200
	--diff_ratio_merging_INS	0.65
	--diff_ratio_filtering_INS	0.65
	--diff_ratio_filtering_DEL	0.35

Datasets generated from cuteSV

We provided the SV callsets of the HG002 human sample produced by cuteSV form three different long-read sequencing platforms (i.e. PacBio CLR, PacBio CCS, and ONT PromethION).

You can download them at:

Please cite the manuscript of cuteSV before using these callsets.

Changelog

cuteSV (v1.0.2):
1.Improve the genotyping performance and enable it to be default option.
2.Make the description of parameters better.
3.Modify the header description of vcf file.
4.Add two new indicators, i.e., BREAKPOINT_STD and SVLEN_STD, to further characterise deletion and insertion.
5.Remove a few redundant functions which will reduce code readability.

Citation

Long Read based Human Genomic Structural Variation Detection with cuteSV. Tao Jiang, et al. bioRxiv 780700; doi: https://doi.org/10.1101/780700

Contact

For advising, bug reporting and requiring help, please post on Github Issue or contact tjiang@hit.edu.cn.