Jit
Enthusiast computational biologist with business dream !!!
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GMOL: An Interactive Tool for 3D Genome Structure Visualization
By Jit 3140 days agowww.nature.com - GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve...SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.
By Jit 2338 days agosynvisio.github.io - SynVisio lets you explore the results of McScanX a popular synteny and collinearity detection toolkit and generate publication ready images. SynVisio requires two files to run: The simplified gff file that was used as an...Panacus : A Counting Tool for Pangenome Graphs
By Neel 863 days agogithub.com - panacus is a tool for calculating statistics for GFA files. It supports GFA files with P and W lines, but requires that the graph is blunt, i.e., nodes do not overlap and consequently, each link (L) points...From DNA Chaos to a Clear Microbial Story
By BioStar 65 days agoImagine opening a metagenomic dataset and finding millions of DNA fragments, each carrying a tiny piece of information about the microbial world inside a sample. The challenge is not generating the data — it is turning that data into a meaningful...Uncovering Evolution’s Blueprint: How ntSynt Is Changing Comparative Genomics
By Jitendra Narayan 6 days agoOver millions of years, evolution has shaped all life on Earth, leaving clues in the DNA of every organism. While different species look and act very differently, their genomes still hold signs of a shared evolutionary past. These connections show...TelomereHunter
By Jit 3187 days agowww.dkfz.de - TelomereHunter is a tool for estimating telomere content from human whole-genome sequencing data. It is designed to take BAM files from a tumor and a matching control sample as input. However, it is also possible to run TelomereHunter with one input...RAMI: a tool for identification and characterization of phylogenetic clusters in microbial...
By Jit 3366 days agoacademic.oup.com - RAMI, which clusters related nodes in a phylogenetic tree based on the patristic distance. RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly. Availability: RAMI is licensed...jobTree based python wrapper to run the genome simulation tool suite Evolver
By Jit 3243 days agogithub.com - evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation...CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies
By Rahul Nayak 3223 days agohttps://cblab.org/camsa/ - CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license. Main features: works with any number of...TAREAN: A computational tool for identification and characterization of satellite DNA from...
By Surabhi Chaudhary 3085 days agobitbucket.org - TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their...
