Jit
Enthusiast computational biologist with business dream !!!
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Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
By Jit 2562 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...INC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 2564 days agogithub.com - INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling...Cerulean: A hybrid assembly using high throughput short and long reads
By Rahul Nayak 2374 days agosourceforge.net - Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 2386 days agogithub.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...Pacasus: Correction of palindromes in long reads from PacBio and Nanopore
By BioStar 2214 days agogithub.com - Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source...Want to Know which genome assembler rule the world ?
Started by Rahul Agarwal 4133 days ago Replies (3) Last reply by Rahul Nayak 2163 days agoAssemblathon 2: evaluating de novo methods of genome...PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead...
By Rahul Nayak 2374 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...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2238 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...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 1769 days agogithub.com - HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation...Porechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 2381 days agogithub.com - Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop...
