Rahul Nayak
A Bioinformatician
Latest comments
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (965 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 (965 days ago): CheckM for...
- Rahul Nayak on CrossMap: program for genome coordinates conversion between different assemblies (1160 days ago): https://www.researchgate.net/publication/357925950_FastRemap_A_Tool_for_Quickly_...
- Rahul Nayak on RGFA: powerful and convenient handling of assembly graphs (1897 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
GenoViz: Visualization software for genomics
By Rahul Nayak 2280 days agosourceforge.net - GenoViz provides software applications and re-usable components for data visualization and data sharing in genomics. Our flagship product is Integrated Genome Browser (IGB).For more information about IGB, visit http://bioviz.org.Source code for...Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
By Rahul Nayak 2296 days agobitbucket.org - Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an...EGAD: Ultra-fast functional analysis of gene networks
By Rahul Nayak 2299 days agogithub.com - With the EGAD (Extending ‘Guilt-by-Association’ by Degree) package, we present a series of highly efficient tools to calculate functional properties in networks based on the guilt-by-association principle. These allow rapid controlled...PilonGrid: parallel wrapper around the Pilon framework
By Rahul Nayak 2300 days agogithub.com - The distribution is a parallel wrapper around the Pilon framework The pipeline is composed of bash scripts, an example mapping.fofn which shows how to input your fastq files (you give paths to the R1 file), and how to launch the...GWASpro: A High-Performance Genome-Wide Association Analysis Server
By Rahul Nayak 2306 days agobioinfo.noble.org - GWASpro supports building complex design matrices, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted for in the linear mixed model (LMM). GWASpro is optimized to handle GWAS data...RopeBWT2: Incremental construction of FM-index for DNA sequences
By Rahul Nayak 2349 days agogithub.com - RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This...Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
By Rahul Nayak 2355 days agosourceforge.net - Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2355 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...RapClust: Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence...
By Rahul Nayak 2369 days agogithub.com - RapClust is a tool for clustering contigs from de novo transcriptome assemblies. RapClust is designed to be run downstream of the Sailfish or Salmon tools for rapid transcript-level quantification. Specifically,...Long read assembly workshop !
By Rahul Nayak 2369 days ago Comments (4)sepsis-omics.github.io - This is a tutorial for a workshop on long-read (PacBio) genome assembly. It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and...
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