Surabhi Chaudhary
A Bioinformatician
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Professor (all levels) in Bioinformatics and Computational Biology
King Abdullah University of Science and Technology (KAUST) (kaust.edu.sa) is seeking a highly motivated and skilled faculty member for the Bioinformatics track whose research focuses on development of methods and tools for Bioinformatics and...EXCAVATOR2tool
By Bulbul 2917 days agosourceforge.net - EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing (WES) data to identify CNVs. EXCAVATOR2 enhances the identification of all genomic CNVs, both overlapping and non-overlapping targeted exons by...The Genome 10K Project
By Jit 3772 days agohttps://genome10k.soe.ucsc.edu The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction...Structural variation: the hidden genomic treasure
By Jit 2906 days ago Comments (6)Structural variants (SVs) such as deletions, insertions, duplications, inversions and translocations litter genomes and are often associated with gene expression changes and severe phenotypes (ie. genetic diseases in humans).QUAST: quality assessment tool for genome assemblies
By Jitendra Prajapati 3154 days ago Comments (2)bioinformatics.oxfordjournals.org - QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.It can works both with and without a given reference genome.The tool accepts multiple assemblies, thus is suitable for comparison. More...YAHA
By Jit 2866 days agowww.ncbi.nlm.nih.gov - YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments....MetaBAT: An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial...
By Jit 2821 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...ABACAS
By Surabhi Chaudhary 2838 days agoabacas.sourceforge.net - ABACAS is intended to rapidly contiguate (align, order, orientate) , visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. It uses MUMmer to find alignment positions and identify syntenies of assembly...FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads
By Jit 2828 days agokakitone.github.io - FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 2811 days agoStructural variation caller tools using long reads
