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By Rahul Nayak 1898 days agowww.melbournebioinformatics.org.au - Written and maintained by Simon Gladman - Melbourne Bioinformatics (formerly VLSCI) Protocol Overview / Introduction In this protocol we discuss and outline the process of de novo assembly for small to medium sized...Tigers genome sequenced
By Rahul Agarwal 4214 days agoOnly 4.4 percent DNA difference between Tiger and house catsCirclator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2513 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...mScaffolder: A comparative genome scaffolding tool
By Jit 2482 days agogithub.com - A comparative genome scaffolding tool based on MUMmer mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the...NovoGraph: building whole genome graphs from long-read-based de novo assemblies
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The Rogers lab studies evolution of genome structure. We explore the ways that complex mutations like duplications, deletions, rearrangements, and retrogenes can create new genetic material. We study how these new mutations are important for...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 1887 days agogithub.com - HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation...Ancient whole genome duplication (WGD) detection tools !
By Rahul Nayak 1486 days agoThere are two methods for ancient WGD detection, one is collinearity analysis, and the other is based on the Ks distribution map. Among them, Ks is defined as the average number of synonymous substitutions at each synonymous site, and there is...odgi: optimized dynamic genome/graph implementation
By Abhimanyu Singh 1155 days agogithub.com - odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses. Careful encoding of graph entities allows odgi to efficiently...
