Rahul Nayak
A Bioinformatician
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Finishing !!
By Jit 2750 days agowww.cbcb.umd.edu - The process of finishing a genome and moving it from a draft stage (the result of sequencing and initial assembly) to a complete genome is typically a time and resource intensive task. The advent of new sequencing technologies...PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 2555 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2381 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...Installing Salmon for Trinity !
By Rahul Nayak 2341 days ago Comments (1)Installing Trinity dependencies !AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2306 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 2010 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...
