Jit
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HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures
By Poonam Mahapatra 1644 days agohuanglab.phys.hust.edu.cn - The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users...Classification of SARS-CoV2 Variant !
By Jit 1104 days agoThe scientists established some guidelines for determining whether a variant is a legitimate branch of an existing lineage:LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 1752 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
By Neel 976 days agogithub.com - Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the...JBrowse 2: a modular genome browser with views of synteny and structural variation
By Abhi 589 days agogithub.com - 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...Genome STRiP
By Neel 3012 days agosoftware.broadinstitute.org - Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals.Genome STRiP...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 2821 days agoStructural variation caller tools using long readsmrFAST: Micro Read Fast Alignment Search Tool
By Neel 3145 days agomrfast.sourceforge.net - mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold,...mafTools
By Radha Agarkar 3119 days agogithub.com - Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.SpeedSeq
By Jit 2876 days agogithub.com - A flexible framework for rapid genome analysis and interpretation C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth...
