Jit
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UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and...
By BioStar 795 days agoikim-essen.github.io - UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment Using state of the art tools, easily extended for other viruses Tool and database updates for critical components via...Early Genome Screening: The New Health Horoscope!
By LEGE 645 days agoAs genome screening becomes more affordable and integrated into routine healthcare, its potential to transform lives is immense. Policymakers, healthcare providers, and genetic counselors must collaborate to ensure ethical implementation, public...PG2: Making Pangenome Graphs Easier to Understand
By Jitendra Narayan 53 days agoGenomics is moving beyond the traditional approach of studying DNA using a single reference genome. Today, researchers are increasingly using pangenomes, which represent genetic information from multiple genomes and capture a much broader range of...The Atlas of Nine Billion Possibilities
By Jitendra Narayan 31 days agoThis question led to the AlphaGenome Atlas (https://deepmind.google.com/science/alphagenome/atlas?), a detailed map of nearly every possible single-letter change in the human genome. Instead of checking each change one by one, researchers can use...Finding the Hidden Switches: The Story of KiNext and Protein Kinases
By LEGE 16 days agoEvery newly sequenced genome contains thousands of proteins, but identifying what each protein does is a much harder task. Among these proteins are protein kinases, important molecular regulators that control processes such as cell growth,...ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
By Seema Singh 3085 days agogithub.com - ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper...GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
By Abhimanyu Singh 3427 days agogithub.com - GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which...ARC: pipeline which facilitates iterative, reference guided de novo assemblies
By Jit 2998 days agoibest.github.io - ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of: Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble...Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 2292 days agogithub.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...mixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 2241 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...
