Rahul Nayak
A Bioinformatician
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Bioinformatics tools for telomere to telomere assembly !
By BioStar 1663 days agooptimize HiFi readsBioKit: a set of tools dedicated to bioinformatics, data visualisation
By Neel 628 days agobiokit.readthedocs.io - BioKit is a set of tools dedicated to bioinformatics, data visualisation (biokit.viz), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis...GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
By Abhimanyu Singh 3211 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...Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 2076 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...miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 3023 days agogithub.com - Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2697 days agogithub.com - new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 2437 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...Supernova: generates phased, whole-genome de novo assemblies from a Chromium-prepared library.
By Jit 2107 days agosupport.10xgenomics.com - Supernova generates phased, whole-genome de novo assemblies from a Chromium-prepared library. Please see Achieving Success with De Novo Assembly and System Requirements before creating your Chromium libraries for...PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead...
By Rahul Nayak 2833 days agogithub.com - PERGA - Paired End Reads Guided Assembler PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds. Instead of using single-end reads to construct...Tigers genome sequenced
By Rahul Agarwal 4554 days agoOnly 4.4 percent DNA difference between Tiger and house cats
