Rahul Nayak
A Bioinformatician
Latest comments
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (837 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 (837 days ago): CheckM for...
- Rahul Nayak on CrossMap: program for genome coordinates conversion between different assemblies (1032 days ago): https://www.researchgate.net/publication/357925950_FastRemap_A_Tool_for_Quickly_...
- Rahul Nayak on RGFA: powerful and convenient handling of assembly graphs (1769 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
VCF Compare !
By Rahul Nayak 1039 days agowiki.bits.vib.be - compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep...DEG 5.0: a database of essential genes in both prokaryotes and eukaryotes
By Rahul Nayak 1334 days agowww.essentialgene.org - Essential genes are those indispensable for the survival of an organism, and their functions are therefore considered a foundation of life. Determination of a minimal gene set needed to sustain a life form, a fundamental question in biology, plays a...DEG 5.0: a database of essential genes in both prokaryotes and eukaryotes
By Rahul Nayak 1334 days agowww.essentialgene.org - Essential genes are those indispensable for the survival of an organism, and their functions are therefore considered a foundation of life. Determination of a minimal gene set needed to sustain a life form, a fundamental question in biology, plays a...AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
By Rahul Nayak 1350 days agogithub.com - AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More...Flanker
By Rahul Nayak 1364 days agogithub.com - Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be...FastProNGS: fast preprocessing of next-generation sequencing reads
By Rahul Nayak 1428 days agogithub.com - FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by...GEO2R: compare two or more groups of Samples
By Rahul Nayak 1434 days agowww.ncbi.nlm.nih.gov - GEO2R to compare two or more groups of Samples in order to identify genes that are differentially expressed across experimental conditions.BioJupies: Automatically Generates RNA-seq Data Analysis Notebooks
By Rahul Nayak 1434 days agoamp.pharm.mssm.edu - With BioJupies you can produce in seconds a customized, reusable, and interactive report from your own raw or processed RNA-seq data through a simple user interface BioJupies now supports user accounts! Sign in from the top right corner of the page...Caretta – A multiple protein structure alignment and feature extraction suite
By Rahul Nayak 1436 days agowww.bioinformatics.nl - Caretta – a multiple protein structure alignment and feature extraction suite Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments...GRIDSS: the Genomic Rearrangement IDentification Software Suite
By Rahul Nayak 1651 days agogithub.com - GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants...
