Long Read Based SV Calling Tools Analysis

Table of Contents

1. Intro
2. Related Datasets and Softwares
   1. Datasets
   2. Aligners
   3. Assemblers
   4. SV Callers
   5. SV Evaluators
3. Analysis Code Readme
4. Data Availability

Intro

In this project, we comprehensively evaluated the performance of 16 long read based SV calling methods along with 4 upstream aligners and 7 assemblers, and offered guidelines and recommendations under 28 criteria for users to select the optimal tools based on different scenarios and directions for further method development. The pipeline of our evaluation was shown as below:

Data Availability

All VCF files generated for evaluation can be found zenodo.

Citation:

Liu YH, Luo C, Golding SG, Ioffe JB, Zhou XM. Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data. Nat Commun. 2024 Mar 19;15(1):2447. PubMed PMID: 38503752.