Rahul Nayak
A Bioinformatician
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npScarf: Scaffolding and Completing Assemblies in Real-time Fashion
By Jit 2740 days agogithub.com - npScarf (jsa.np.npscarf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbial datasets. It...WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.
By Neel 1156 days agohuttenhower.sph.harvard.edu - Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While methods exist to identify LGTs from sequenced isolate genomes, identifying LGTs from community...GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or...
By Shruti Paniwala 2356 days agoacademic.oup.com - GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap...GFinisher: a new strategy to refine and finish bacterial genome assemblies
By Jit 2311 days agogfinisher.sourceforge.net - GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar...NovoGraph: building whole genome graphs from long-read-based de novo assemblies
By Jit 2199 days agogithub.com - NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of...Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 1605 days agogithub.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
By Neel 918 days agogithub.com - The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is...poRe: an R package for the visualization and analysis of nanopore sequencing data
By Jit 2556 days ago Comments (1)academic.oup.com - Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the...GPOPSIM: a simulation tool for whole-genome genetic data
By Jit 2501 days agogithub.com - GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can...AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Jit 2338 days ago Comments (1)github.com - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC...
