vsFilt: A tool to improve virtual screening by structural filtration of docking poses
The vsFilt is the first open application for post-docking structural filtration, available as a web-server. The new tool is easy to use and configure to detect a wide range of interaction types that are known to be involved in molecular recognition, including hydrogen and halogen bonds, ionic int...Tags: vsFilt, tool, improve, virtual, screening, structural, filtration, docking, poses
1255 days ago
Tags: Syri, compares, alignments, chromosome-level, assemblies, synteny, structural, rearrangements
702 days ago
JASMINE: Jointly Accurate Sv Merging with Intersample Network Edges
This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a netw...Tags: JASMINE, Accurate, SV, Merging, Intersample, Network, Edges, structural, variants
670 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 have an increased fetchSizeLimit (which is otherwise git in CRAM longread tests) jb2-web - stock instance of jbrowse-web v1.7.5 jb1 - stock instance...Tags: JBrowse, modular, genome, browser, views, synteny, structural, variation
373 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/normal analysis, supports multiple tumor samples, and produces accurate and complete somatic and germline calls. Severus takes advantage of long-read phasing and uses the ...Tags: Severus, somatic, structural, variation, SV, caller, long reads
33 days ago
Minda: a tool for evaluating structural variant (SV) callers
Minda is a tool for evaluating structural variant (SV) callers that standardizes VCF records for compatibility with both germline and somatic SV callers, benchmarks against a single VCF input file, or benchmarks against an ensemble call set created from multiple VCF input files.Tags: Minda, tool, evaluating, structural, variant, SV, callers
33 days ago
Tags: SViper, Swipe, Structural, Variants, ONT, PacBio, reads, Illumina
1594 days ago
SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window (wi...Tags: SvABA, Structural, variation, indel, detection, local, assembly
1515 days ago
SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
SVEngine (Structural Variants Engine) SVEngine is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios. SVEngine takes as input reference contigs in FASTA files, variant meta ...Tags: SVEngine, Allele, Haplotype, Aware, Structural, Variants, Simulator, Simulation
1399 days ago
truvari: Structural variant comparison tool for VCFs
Structural variant comparison tool for VCFs Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure. Spiral Genetics MotivationTags: truvari, Structural, variant, comparison, tool, VCFs
1402 days ago