Rahul Nayak
A Bioinformatician
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Bioinformatics tools for genome assembly !
Last updated 1168 days ago by BioStarThere are numerous genome assembly tools available, each with its strengths and weaknesses. Here is a list of some widely used genome assembly tools as of my last update in September 2021: SPAdes: An assembler specifically designed for...-
Software packages for next gen sequence analysis
Last updated 4124 days ago by Rahul Nayak Comments (5)Integrated solutions * CLCbio Genomics Workbench - de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection,... LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
By Jit 3065 days agoshendurelab.github.io - LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available...-
Comprehensive list of visualization tools for biological pathways
Last updated 3169 days ago by NeelThe study of biological pathways is a key to understand the different processes inside a cell: proteins exert their function not in isolation but in a tightly controlled network of interactions and reactions. Activation of a pathway typically leads... List of popular bioinformatics software/tools
By Jitendra Narayan 4828 days ago Comments (28)samtools.sourceforge.net - In current genome era, our day to day work is to handle the huge geneome sequences, expression data, several other datasets. This link provide a comprehensive list of commonly used sofware/tools.Software developed in pevsner lab
By Robert M Willioms 4381 days agopevsnerlab.kennedykrieger.org - DRAGON: Database Referencing of Array Genes Online SNOMAD: Standardization and Normalization of Microarray Data SNPduo: SNP Analysis Between Two Individuals SNPtrio: Analyzing and Visualizing and Inheritance Patterns in Trios SNPscan: Data...EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
By Rahul Nayak 3071 days agoarthropods.eugenes.org - EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University,...Spines
By Jitendra Narayan 3890 days agowww.broadinstitute.org - Spines Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments,...wgd—simple command line tools for the analysis of ancient whole-genome duplications
By LEGE 2264 days agogithub.com - wgd is a easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and colinearity analysis workflows together with tools for modeling and visualization, rendering these...
