Results for "Structural"
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TARDIS: Toolkit for automated and rapid discovery of structural variants
tardis Toolkit for Automated and Rapid DIscovery of Structural variants Requirements zlib (http://www.zlib.net)mrfast (https://github.com/BilkentCompGen/mrfast)htslib (included as submodule; http://htslib.org/)Fetching tardis git clone https://github.com/BilkentCompGen/tardis.git --recursive ...Tags: TARDIS, Toolkit, automated, rapid, discovery, structural, variants
2526 days ago
- Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels ...
Tags: Manta, rapid, detection, structural, variants, indels, germline, cancer, sequencing, applications
2173 days ago
NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different analysis purpose. The output of NextSV is in AN...Tags: NextSV, meta-caller, structural, variants, low-coverage, long-read, sequencing, data
2102 days ago
- This is a tool for detecting structural variations using soft-clipping information From SAM files. https://github.com/shinout/clipcrop
Tags: ClipCrop, tool, detecting, structural, variations, single-base, resolution, soft-clipping, information
2043 days ago
- ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data – SV len...
Tags: ClipCrop, tool, detect, structural, variations, single-base, resolution, soft-clipping, information
1936 days ago
SvABA: Genome-wide detection of structural variants and indels 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, Genome-wide, detection, structural, variants, indels, local, assembly
1934 days ago
GMASS: a novel measure for genomeassembly structural similarity
The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2710-zTags: GMASS, novel, measure, genome, assembly, structural, similarity
1851 days ago
GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns
GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction. GSP4PDB is part of the services provided by the Bioinformatic Group of the University of Talca http://gdblab.com/gsp4pdb/gsp4pdb2/ https://bmcbioinformati...Tags: GSP4PDB, web, tool, visualize, search, explore, protein-ligand, structural, patterns
1516 days ago
- Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a region, Inversions of a region, or Translocations ...
Tags: Parliament2, structural, variant, calls, whole-genome, sequencing, data, NGS
1441 days ago
chromatiblock: Scalable, whole-genome visualisation of structural changes in prokaryotes
To create a fresh environment for chromatiblock to run in do: conda create --name chromatiblock conda activate chromatiblock conda install chromatiblock --channel conda-forge --channel bioconda Then in future to run chromatiblock you can reactivate this environemtn using conda activate...Tags: chromatiblock, Scalable, whole-genome, visualisation, structural, changes, prokaryotes, synteny
1354 days ago
