Rahul Nayak
A Bioinformatician
Latest comments
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (836 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (836 days ago): CheckM for...
- Rahul Nayak on CrossMap: program for genome coordinates conversion between different assemblies (1031 days ago): https://www.researchgate.net/publication/357925950_FastRemap_A_Tool_for_Quickly_...
- Rahul Nayak on RGFA: powerful and convenient handling of assembly graphs (1767 days ago): The Graphical Fragment Assembly (GFA) is a proposed format which allow to...
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Genome, Assembly, reads, analysis, NGS, de novo, Tools, Bioinformatics, tool, visualization, data, R, sequencing, Pipeline, Computational Biology, Long, Assemblies, fast, AligNment, annotation, assembler, genomes, Software, MUltiple, Python, genes, database, Genomics, Tutorial, Education, scaffolding, transcriptome, Nanopore, fastq, Perl, Merging, Solution, Tree, Network, Resolution, U-Plot, gene, Bacteria, gap, Genomic, structure, Elements, mapping, Suite, system
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Rahul Nayak's bookmarks
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
By Rahul Nayak 2333 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...CGView - Circular Genome Viewer
By Rahul Nayak 2346 days agowishart.biology.ualberta.ca - CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature...Cerulean: A hybrid assembly using high throughput short and long reads
By Rahul Nayak 2361 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...PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead...
By Rahul Nayak 2361 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...kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
By Rahul Nayak 2368 days agogithub.com - The k-mer Weighted Inner Product. This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any...Porechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 2368 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...CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and...
By Rahul Nayak 2374 days ago Comments (2)ecogenomics.github.io - CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous...bpRNA: large-scale automated annotation and analysis of RNA secondary structure
By Rahul Nayak 2374 days agogithub.com - bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with...MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 2386 days agogithub.com - MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and...MIX: Combining multiple assemblies from NGS data
By Rahul Nayak 2389 days agogithub.com - Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices...
