Non-allelic homologous recombination (NAHR) is a common mechanism for generating genome rearrangements and is implicated in numerous genetic disorders, but its detection in high-throughput sequencing data poses a serious challenge.
Leverages a breakpoint junction library for structural variants (SVs) detection. BreakSeq is an approach that identifies SVs by aligning raw reads directly onto SV breakpoint junctions of the alternative, non-reference, alleles contained in a library. The software can serve for identifying specific SV alleles in personal genomics data. It enables a step towards overcoming reference biases.
Detects non-allelic homologous recombination (NAHR) from short-read data. detect-NAHR is a Bayesian algorithm that probabilistically models NAHR based on the rules of the mechanism and employs a specifically designed hidden Markov model alignment algorithm to probabilistically compare reads among repetitive sequences.
Detects homologous recombination events from single-nucleotide polymorphism (SNP) data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. HREfinder is intended for hypothesis generation, and should be followed up by more detailed analyses of sequences, not just SNPs, to verify predicted HREs. HREfinder is intended to be used as a tool for hypothesis generation, so results are best interpreted and verified by more detailed analyses of the HRE predictions.
Finds and genotypes non-allelic homologous recombination (NAHR) mediated inversions from long read sequencing data. npInv analyzes an alignment file for reads that provide pairs of subread alignments mapping to the same chromosome. It employs inversion signals to discover into inversion event based on position and the number of inversion signals in a defined cluster. This tool aims to improve the understanding of the extent of inversion polymorphisms, their evolutionary significance and their clinical impact.