Rahul Nayak
A Bioinformatician
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AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2307 days agowww.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2233 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...snakepipes: A toolkit based on snakemake and python for analysis of NGS data
By Jit 2011 days agogithub.com - snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data. DNA-mapping* ChIP-seq* RNA-seq* ATAC-seq* scRNA-seq Hi-C Whole Genome Bisulfite Seq/WGBS (*Also available in...The Minerva Research Group for Bioinformatics
The focus of the bioinformatics group is to use computational approaches to gain an insight into genome evolution in primates. http://www.eva.mpg.de/genetics/bioinformatics/overview.html?Fsize=0%2C%20%40%2F%27 Kelso Group Department of...gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
By Rahul Nayak 1771 days agogithub.com - gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and...Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome...
By Jit 1646 days agogithub.com - Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a...Understanding HiFi Reads !
By Rahul Nayak 981 days agopacb.com - While little public data is available for either of the new synthetic long read approaches, Illumina showed an example comparison earlier this year at the Festival of Genomics & Biodata conference (FoG 2022). In the IGV screenshot...1mb long DNA with Nanopore technology
By Jit 2537 days agoLongest read of 1mb achievements with NanoporePacasus: Correction of palindromes in long reads from PacBio and Nanopore
By BioStar 2209 days agogithub.com - Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source...ngs-bits - Short-read sequencing tools
By Neel 1779 days agogithub.com - Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources: Binaries for Linux/macOS From sources for Linux/macOS From sources for Windows
