A full list of software can be found here.
ClipSV
ClipSV is a novel method for SV detection based on read extension, spliced alignment, and local assembly. The source code and documentation can be downloaded here. Write to Peng Xu should you have any questions.
MRLR
MRLR is a pipeline to identify meiotic recombination events using trio samples of whole genome 10X Genomics sequencing data. The source code and documentation can be downloaded here. Write to Peng Xu if you have any questions.
novoBreak
novoBreak (Chong et al. 2017) is a tool for structural variations (deletions, duplications, inversions, translocations) detection on Illumina sequencing data. This tool has won several rounds of participated ICGC-TCGA DREAM Mutation Calling Challenge SV Sub-challenge. The source code, binary executable package and documentation can be downloaded here. Write to Zechen Chong if you have any questions.
Rainbow
Rainbow (Chong et al. 2012) is a tool for efficient clustering and assembling RAD-seq reads. The source code and documentation can be downloaded here. Write to Zechen Chong or Jue Ruan if you have any questions.
