Structural variant analysis Tools

A high-speed next-gen sequencing structural variation caller. It calls variants based on alignment-guided positional de Bruijn graph breakpoint assembly, split read, and read pair evidence.

GangSTR is a tool for genome-wide profiling tandem repeats from short reads. A key advantage of GangSTR over existing genome-wide TR tools is that it can handle repeats that are longer than the read length. GangSTR takes aligned reads (BAM) and a set of repeats in the reference genome as input and outputs a VCF file containing genotypes for each locus.

Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads.

The Long Read Aligner for Sequences and Contigs. LRA, the long read aligner for sequences and assembly contigs LRA is a sequence alignment program that aligns long reads from single-molecule sequencing (SMS) instruments, or megabase-scale contigs from SMS assemblies. LRA implements seed chaining sparse dynamic programming with a convex gap function to read and assembly alignment, which is also extended to allow for inversion cases. Through the Truvari analysis of LRA, Minimap2 and NGM-LR alignments. LRA achieves higher f1 score over HG002 HiFi, CLR and ONT datasets. Home: https://github.com/ChaissonLab/LRA. Long read aligner for sequences and contigs.