Rahul Nayak
A Bioinformatician
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Genetic-mapper: SVG Genetic Map Drawer
By Jit 2714 days agogithub.com - Genetic-mapper is a perl script able to draw publication-ready vectorial genetic maps. Perl script for creating a publication-ready vectorial genetic/linkage map in Scalable Vector Graphics (SVG) format. The resulting file can either be submitted...Creating Genetic Maps from GBS data
By BioStar 441 days agobioinformaticsworkbook.org - Genetic map, as the name suggest is simply knowing the relative positions of specific sequences across the genome. There are various methods to generate them, but most popular method is to use a cross between the known parents and examining their...Flanker
By Rahul Nayak 1364 days agogithub.com - Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be...SKESA: strategic k-mer extension for scrupulous assemblies
By Jit 2200 days agogithub.com - SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity,...Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
By Neel 964 days agogithub.com - Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the...LAST
By Bulbul 2895 days agohttp://last.cbrc.jp/ - LAST can: Handle big sequence data, e.g: Compare two vertebrate genomes Align billions of DNA reads to a genome Indicate the reliability of each aligned column. Use sequence quality data properly. Compare DNA...PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 2548 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation
By Shruti Paniwala 911 days agogitlab.com - CrowdGO is a protein Gene Ontology predictor using a meta approach, analyzing the predictions of other tools in order to get an improved precision and recall. Please note that the CrowdGO snakemake workflow is currently only tested on Ubuntu. It...Platanus
By Jit 3115 days ago Comments (1)platanus.bio.titech.ac.jp - Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data. The latest version is 1.2.4. To cite Platanus, please use the...Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 2522 days agogithub.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in...
