Rahul Nayak
A Bioinformatician
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AMStat: display statistics of large sequence files from next generation sequencing projects
By Neel 2886 days agosamstat.sourceforge.net - SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads...EXCAVATOR: detecting copy number variants from whole-exome sequencing data
By Radha Agarkar 2830 days agosourceforge.net - EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies...jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
By Abhimanyu Singh 2627 days agogithub.com - jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants...DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 2444 days agogithub.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome...
By Jit 2320 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...Figeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 747 days agogithub.com - Tool for plotting sequencing data along genomic coordinates. FIGENO is a FIGure GENerator for GENOmics With figeno, you can plot various types of sequencing data along genomic coordinates. Video...Scallop: reference-based transcriptome assembler for RNA-seq
By Rahul Nayak 3071 days agogithub.com - Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be...List of gene ontology software and tools
By Jit 4592 days ago Comments (9)The list of most commonly used old and new GO term enrichment determination toolsHiCdat
By Jit 3887 days agogithub.com - HiCdat: a fast and easy-to-use Hi-C data analysis tool HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes,...FUMA GWAS: Functional Mapping and Annotation of Genome-Wide Association Studies
By Jit 2682 days agohttps://fuma.ctglab.nl/ - FUMA is a platform that can be used to annotate, prioritize, visualize and interpret GWAS results. The SNP2GENE function takes GWAS summary statistics as an input, and provides extensive functional annotation for all SNPs in genomic...
