Jitendra Narayan
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Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences
By Jit 3851 days agobioinformatics.ua.pt - Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For...Professor/Senior Lecturer of Comparative Genomics @ University of Glasgow
University of Glasgow College of Medical, Veterinary and Life Sciences School of Biodiversity, One Health and Veterinary Medicine Professor/Senior Lecturer of Comparative Genomics Vacancy Ref: 153610 Salary: Professor, Grade 10 will be within...MEDEA: Comparative Genomic Visualization with Adobe Flash
By Jit 3851 days agowww.broadinstitute.org - As the number of sequence and annotated genomes grows larger, the need to understand, compare, and contrast the data becomes increasingly important. Using the power of the human visual system to detect trends and spot outliers is necessary in such...JCVI utility libraries
By Jit 2013 days agogithub.com - Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.Public Databases for Bioinformatics !
By Jit 2059 days agomitra.stanford.edu - https://www.nature.com/articles/s41467-020-17155-yServer Infrastructure: File Server: dhara: Synology 3614 Storage Appliance 4 Core Xeon 108TB disk storage 10Gb ethernet to SCG3 Access atx: dhara:5000 Has btsync server (try it - its much...Ribbon: Visualizing complex genome alignments and structural variation:
By Jit 3269 days agohttp://genomeribbon.com/ - Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right. Local installation: You can install Ribbon...jobTree based python wrapper to run the genome simulation tool suite Evolver
By Jit 3260 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...Mash: fast genome and metagenome distance estimation using MinHash
By Jit 3256 days agogithub.com - Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is...GIGGLE: a search engine for large-scale integrated genome analysis
By Jit 3227 days agogithub.com - GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is...
