Surabhi Chaudhary
A Bioinformatician
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SNPGenie
By Jit 3480 days agogithub.com - SNPGenie is a Perl script for estimating evolutionary parameters, mainly from pooled next-generation sequencing (NGS) single-nucleotide polymorphism (SNP) variant data. SNP reports (acceptable in a variety of formats) much each correspond to a...Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
By Shruti Paniwala 2906 days agowww.well.ox.ac.uk - Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect...DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
By Jit 2033 days ago Comments (1)github.com - DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools...VG: variation graph data structures, interchange formats, alignment, genotyping, and variant...
By Jit 2446 days agogithub.com - Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: nodes, which are labeled by sequences and ids edges, which connect two nodes via either of...GWASpro: A High-Performance Genome-Wide Association Analysis Server
By Rahul Nayak 2863 days agobioinfo.noble.org - GWASpro supports building complex design matrices, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted for in the linear mixed model (LMM). GWASpro is optimized to handle GWAS data...Tools to detect synteny blocks regions among multiple genomes
By Jitendra Narayan 4771 days ago Comments (24)Collections of synteny detection tools and related materialsIQ-TREE: Efficient software for phylogenomic inference
By Jit 2790 days agohttp://www.iqtree.org/ - A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time IQ-TREE found higher likelihoods between 62.2%...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1687 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...R package for visualising GO enrichment
By Jit 4827 days agoR package for visualising GO enrichment results as wordclouds is available at CRANRNA-Seq Data Pathway and Gene-set Analysis Workflows
By Jit 4732 days agoDescribe the GAGE workflows on RNA-Seq data pathway analysis and gene-set analysis.
