|Copy number variation (CNV) is a type of structural variation, specifically, it is a type of duplication or deletion events. During the last month, the Galaxy community has cooperated with the CNV community to bring a variety of the best CNV tools to the Galaxy ecosystem. In addition, we updated the variant calling tools, specifically to also cope with long read sequencing technologies.|
In the following, you will find a list of a few highlights. We would like to thank all contributors, especially Nathan Roach, Niko Pinter, Stephan Flemming and the ELIXIR CNV community.
is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. [Project link] [Galaxy tool]
is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. [Project link] [Galaxy tool]
is 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 employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. [Project link] [Galaxy tool]
is a tool to create consensus sequences and variant calls from nanopore sequencing data using neural networks applied a pileup of individual sequencing reads against a draft assembly. [Project link] [Galaxy tool]
calls somatic short mutations via local assembly of haplotypes. Short mutations include single nucleotide (SNA) and insertion and deletion (indel) alterations. The caller uses a Bayesian somatic genotyping model. [Project link] [Galaxy tool]