Surabhi Chaudhary
A Bioinformatician
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splitbam: splits a BAM by chromosomes
By Jit 2824 days agocode.google.com - splitbam splits a BAM by chromosomes. Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to...QuorUM: An Error Corrector for Illumina Reads
By Jit 2571 days agojournals.plos.org - Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 × coverage Illumina data on average has an error in some read...NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
By BioStar 2129 days agogithub.com - NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file...vcfR: a package to manipulate and visualize VCF data in R
By Jit 2220 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 1705 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 2818 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...vsFilt: A tool to improve virtual screening by structural filtration of docking poses
By Neel 1458 days agobiokinet.belozersky.msu.ru - The vsFilt is the first open application for post-docking structural filtration, available as a web-server. The new tool is easy to use and configure to detect a wide range of interaction types that are known to be involved in molecular recognition,...Cancer Dependency Map
By Jit 1744 days agodepmap.sanger.ac.uk - The consequences of alterations in the DNA of cancer cells and subsequent vulnerabilities are not fully understood. This project aims to assign a dependency to every cancer cell in a patient which could be exploited to develop new therapies. This...Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
By Jit 1718 days agogithub.com - A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg) Link to working demo:...NGS course Medical Genomics, scheduled for 17-20 September 2013 in UZ Leuven (Belgium).
By Poonam Mahapatra 4120 days agoThe 4-day course is organized as a series of morning lectures and afternoon hands-on workshops.
