SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data u...ing Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....use only clipped, discordant, unmapped and indel reads, although this ca...realigned to the contigs with BWA-MEM, and var...1530 days ago
1472 days ago
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rea...-wide break-end assembler, as well as a structural variation caller for Illumina seq...graph genome-wide break-end assembly, split read, and rea...1462 days ago
pggb: the pangenome graph builder
This pangenome graph construction pipeline renders a collection of sequ...into a pangenome graph (in the variation graph model). Its goal is to...graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local line...interpretation, visualization, and reu...1343 days ago
DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms
DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorp...SP can estimate several measures of DNA sequence variation within and between populations in noncod...linkage disequilibrium, recombination, gene flow and gen...1270 days ago
Applied Computational Genomics Course at UU: Spring 2020
This course will provide a comprehensive introduction to fundamental concepts and experimental approaches in the analysis and interpretation of experimental...lectures covering key concepts and analytical strategies. A dive..., the identification of genetic variation, structural variation, and ChI...1242 days ago
Collection of Graph Visualization tools !
Standard approaches to genome inference and analysis relate sequences to a single linear reference genome. This...amental problem: Differences from this reference are hard to observe and describe in a coherent way. Variati...479 days ago
JBrowse 2: a modular genome browser with views of synteny and structural variation
igvjs - a create-react-app with igv package from npm installed. the igv.js is instrumented to output "DONE" to the console when finished, and to...389 days ago
Severus: a somatic structural variation (SV) caller for long reads
Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT). It is designed for matching tumor/nor...analysis, supports multiple tumor samples, and produces accurate and complet...everus takes advantage of long-read phasing and use...49 days ago