Next Generation Sequencing (NGS)
Rahul Agarwal 4617 days ago
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Figeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 536 days agogithub.com - Tool for plotting sequencing data along genomic coordinates. FIGENO is a FIGure GENerator for GENOmics With figeno, you can plot various types of sequencing data along genomic coordinates. Video...
Commercial and public next-gen-seq (NGS) software
Last updated 4190 days ago by Partek Comments (7)Integrated solutions CLCbio Genomics Workbench - de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection,...kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference...
By Jit 3011 days agosourceforge.net - Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages...RAINBOWR: Reliable Association INference By Optimizing Weights with R (R package for SNP-set GWAS...
By Surabhi Chaudhary 2198 days agogithub.com - RAINBOWR(Reliable Association INference By Optimizing Weights with R) is a package to perform several types of GWAS as follows. Single-SNP GWAS with RGWAS.normal function SNP-set (or gene set) GWAS with RGWAS.multisnp function (which tests...DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
By Jit 1817 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 2230 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...Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?
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