Surabhi Chaudhary
A Bioinformatician
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karyoploteR: plot whole genomes with arbitrary data
By Abhimanyu Singh 2490 days agobernatgel.github.io - karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR...Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 2414 days agogithub.com - Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls...Epiviz: an interactive visualization tool for functional genomics data.
By Jit 2333 days agohttps://epiviz.github.io/ - Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other...VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
By Rahul Nayak 2246 days agogithub.com - VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store...EXCAVATOR: detecting copy number variants from whole-exome sequencing data
By Radha Agarkar 2154 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...nQuire: A statistical framework for ploidy estimation using NGS short-read data
By Jit 2127 days agogithub.com - nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish...Trelliscope: flexibly visualize large, complex data in great detail from within the R statistical...
By Jit 1772 days agodeltarho.org - Trelliscope provides a way to flexibly visualize large, complex data in great detail from within the R statistical programming environment. Trelliscope is a component in the DeltaRho environment. For those familiar with Trellis...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 1744 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome...
By Jit 1644 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...DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
By Jit 1478 days agobenjjneb.github.io - The DADA2 tutorial goes through a typical workflow for paired end Illumina Miseq data: raw amplicon sequencing data is processed into the table of exact amplicon sequence variants (ASVs) present in each sample. The DADA2...
