Rahul Nayak
A Bioinformatician
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Hapsembler: An Assembler for Highly Polymorphic Genomes
By Jit 2846 days agocompbio.cs.toronto.edu - Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454....Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit,...
By Neel 2220 days agowww.phrap.org - Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence...NCBI Datasets pages
By BioStar 969 days agoAssembly and Genome record pages now redirect to new NCBI Datasets pages.Step-by-Step Guide to Running Genome Assembly
By Abhi 449 days agoGenome assembly is a powerful process that transforms raw sequencing data into a coherent representation of an organism’s genome. By following this step-by-step guide, you can successfully assemble genomes and uncover valuable biological insights....
My commonly used commands in Bioinformatics
Last updated 2781 days ago by Rahul NayakFYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta...AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome...
By Jit 2266 days agogithub.com - We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.How to sequence the human genome - Mark J. Kiel
By Rahul Nayak 4299 days agoView full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological...A 3D Map of the Human Genome
By Jitendra Narayan 4103 days agoSuhas Rao and Miriam Huntley (of the Aiden Lab) describe a 3D map of the human genome at kilobase resolution, revealing the principles of chromatin looping. Guest Origami Folding: Sarah Nyquist. Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand,...Genome Stability Laboratory
The bakers yeast, Saccharomyces cerevisiae is an ideal model organism to understand mechanisms of meiotic chromosome segregation. In S. cerevisiae and in mammals, the majority of meiotic crossovers are formed through a highly conserved MSH4p-MSH5p,...
