BioStar
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Genobuntu: Package for Next Generation Sequencing and Genome Assembly
By BioStar 1680 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...QuasiModo - Quasispecies Metric Determination on Omics
By Neel 1276 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...lsugenomics Lab
In our lab, we seek to characterize and to compare genomes in order to better understand genetic and evolutionary processes linking genotypes to phenotypes. Sequencing and decoding plant genomes have been integral in our approaches. The...Proksee
By LEGE 271 days agohttps://proksee.ca/ - Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file. Please Cite the Following Grant JR, Enns E, Marinier E,...Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Rahul Nayak 2597 days agogithub.com - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq dataAfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good...MinION_GC: An R script to do some QC on MinION data
By Radha Agarkar 2577 days agogithub.com - Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out...MIX: Combining multiple assemblies from NGS data
By Rahul Nayak 2421 days agogithub.com - Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices...NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
By Jit 2331 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...kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
By Jit 2177 days ago Comments (1)pachterlab.github.io - kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for...heatmaply: popular graphical method for visualizing high-dimensional data
By Neel 1808 days agotalgalili.github.io - This work is based on ggplot2 and plotly.js engine. It produces similar heatmaps as d3heatmap, with the advantage of speed (plotly.js is able to handle larger size matrix), and the ability to zoom from the dendrogram. heatmaply also provides an...
