Surabhi Chaudhary
A Bioinformatician
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vcfR: a package to manipulate and visualize VCF data in R
By Jit 2902 days agogithub.com - VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices from...tinycov: standalone command line utility written in python to plot coverage from a BAM file
By Jit 2387 days agogithub.com - Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by Matt Edwards' genome coverage plotter. To install the stable version: pip3 install --user...MetaBAT: An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial...
By Jit 3500 days agobitbucket.org - MetaBAT, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome...ViralQC: Checking If a Viral Genome Tells the Whole Story
By LEGE 27 days agoViral sequences recovered from metagenomic data can be incomplete or contaminated with microbial DNA. ViralQC uses information from both DNA sequences and predicted proteins to detect contamination and estimate how complete a viral contig is.irishgrid: Irish Grid Mapping System
By Jit 4301 days agocode.google.com - Perl module for creating geographic 10km-square maps using either SVG or PNG (with GD library) output format. Originally design to map the location of objects in a 10 km map IrishGrid includes: native support of the Irish Grid System (see...When Thousands of Bacterial Genomes Become One Giant Map
By LEGE 39 days agoDeveloped by Jérôme Arnoux and colleagues, PANORAMA is a computational tool designed to explore bacterial pangenomes—the complete collection of genetic possibilities found across a species or group of related organisms. Instead of looking at every...Collection of Graph Visualization tools !
By Neel 1349 days agopangenome.github.io - Standard approaches to genome inference and analysis relate sequences to a single linear reference genome. This is efficient but has a fundamental problem: Differences from this reference are hard to observe and describe in a coherent way. Variation...
The genome factory !!!
By Madhvan Reddy 4645 days agoWorld’s first $1,000 genome enables ‘factory’ scale sequencing for population and disease studies
