Next Generation Sequencing (NGS)
Rahul Agarwal 4707 days ago
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Libraries or management tools for high throughput sequencing data
Last updated 610 days ago by LEGEGATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.These methods enable the analysis of data sets of any size on multi-core desktop...-
Software packages for next gen sequence analysis
Last updated 4004 days ago by Rahul Nayak Comments (5)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,... 
Snippy: Rapid haploid variant calling and core SNP phylogeny
By Neel 2855 days agogithub.com - Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is...QuasiModo - Quasispecies Metric Determination on Omics
By Neel 1805 days agogithub.com - This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In this study we evaluated genome assemblers and variant callers on 10 in vitro generated, mixed strain HCMV sequence samples, each...Snakemake workflow: dna-seq-gatk-variant-calling
By Jit 2507 days agogithub.com - This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.Calling variants in non-diploid systems
By Neel 1805 days ago Comments (1)training.galaxyproject.org - The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been...Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?
Rahul Agarwal 4706 days ago320000 viruses in mammals yet to sequenced in future!!!
By Rahul Agarwal 4658 days ago70 per cent of emerging viral diseases such as HIV/AIDS, West Nile, Ebola, SARS, and influenza, are zoonoses - infections of animals that cross into humans.DNA tale of 3 to 4 years old Serbia boy
By Rahul Agarwal 4574 days agoAncient DNA study of Serbian boy!!!
