Rahul Nayak
A Bioinformatician
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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...PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
By Surabhi Chaudhary 2368 days agoderisilab.ucsf.edu - We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively...Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de...
By Jit 1922 days agojournals.plos.org - Chromosome-level genome assembler combining multiple de novo assemblies https://github.com/jkimlab/IMAPProtocol for De novo Genome Assembly using Illumina Reads
By BioStar 1418 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life
By Abhimanyu Singh 2224 days agoancestralgenomes.org - Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these ‘fossil genomes’. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species...Tallymer: method to compute K-mer frequencies and its application to annotate large repetitive...
By Jit 2484 days agowww.zbh.uni-hamburg.de - Tallymer is based on enhanced suffix arrays. This gives a much larger flexibility concerning the choice of the k-mer size. Tallymer can process large data sizes of several billion bases. We used it in a variety of applications to study the...GenomeMapper: Simultaneous alignment of short reads against multiple genomes
By Jit 2385 days ago1001genomes.org - GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 1678 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
By Jit 2737 days agogithub.com - GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.htmlFeatures Mapping position agnostic to alignment parameters. ...EAGLER: a scaffolding tool for long reads.
By Jit 2375 days agogithub.com - EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping...
