Rahul Nayak
A Bioinformatician
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PBSuite: Software for Long-Read Sequencing Data from PacBio
By Jit 2804 days agosourceforge.net - PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads.----- PBJelly -----Read The...Prokka: tool for the rapid annotation of prokaryotic genomes
By Jit 2797 days agowww.vicbioinformatics.com - Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files...COCACOLA (binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and...
By Jit 2796 days agogithub.com - COCACOLA is a general framework that combines different types of information: sequence COmposition, CoverAge across multiple samples, CO-alignment to reference genomes and paired-end reads LinkAge to automatically bin contigs into OTUs. Furthermore,...CABOG: Celera Assembler with Best Overlap Graph
By Abhimanyu Singh 2727 days agowww.jcvi.org - CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as...Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
By Jit 2529 days agoschatzlab.cshl.edu - Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used...MeDuSa: a multi-draft based scaffolder
By Abhimanyu Singh 2452 days agogithub.com - MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa...Installing Bandage on Ubunty !
By Jit 2369 days agoinstructions successfully build Bandage on a fresh installation of Ubuntu 14.04Hapsembler: An Assembler for Highly Polymorphic Genomes
By Jit 2355 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....Protocol for De novo Genome Assembly using Illumina Reads
By BioStar 1385 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.NCBI Datasets pages
By BioStar 478 days agoAssembly and Genome record pages now redirect to new NCBI Datasets pages.
