Rahul Nayak
A Bioinformatician
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k-mers tutorial - classification and taxonomy
By Neel 1184 days agoivory.idyll.org - DNA k-mers underlie much of our assembly work, and we (along with many others!) have spent a lot of time thinking about how to store k-mer graphs efficiently, discard redundant data, and count them efficiently. More recently, we've...Want to Know which genome assembler rule the world ?
Started by Rahul Agarwal 4121 days ago Replies (3) Last reply by Rahul Nayak 2151 days agoAssemblathon 2: evaluating de novo methods of genome...Bandage: interactive visualization of de novo genome assemblies
By Shruti Paniwala 2545 days agorrwick.github.io - Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes,...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Jit 2394 days agogithub.com - Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After...ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
By Rahul Nayak 2334 days agofaculty.cse.tamu.edu - With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2226 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...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2061 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 1783 days agogithub.com - NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate...ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
By LEGE 198 days agogithub.com - ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate...Protocol for De novo Genome Assembly using Illumina Reads
By BioStar 1406 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.
