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odgi: optimized dynamic genome/graph implementation
By Abhimanyu Singh 1708 days agogithub.com - odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses. Careful encoding of graph entities allows odgi to efficiently...
Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?
Rahul Agarwal 4830 days ago320000 viruses in mammals yet to sequenced in future!!!
By Rahul Agarwal 4782 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.Hagfish - assess an assembly through creative use of coverage plots
By Abhi 3791 days agogithub.com - Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or...Genobuntu: Package for Next Generation Sequencing and Genome Assembly
By BioStar 2333 days agosourceforge.net - Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.Commonly used biological software and...MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer...
By Rahul Nayak 1624 days agogithub.com - MUM&Co is able to detect:Deletions, insertions, tandem duplications and tandem contractions (>=50bp & <=150kb)Inversions (>=1kb) and translocations (>=10kb)NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
By Jit 2984 days agogithub.com - NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different...DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 2447 days agogithub.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome...
By Jit 2322 days agogithub.com - Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a...DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
By Jit 2156 days agobenjjneb.github.io - The DADA2 tutorial goes through a typical workflow for paired end Illumina Miseq data: raw amplicon sequencing data is processed into the table of exact amplicon sequence variants (ASVs) present in each sample. The DADA2...
