Jit
Enthusiast computational biologist with business dream !!!
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e-RGA: enhanced Reference Guided Assembly of Complex Genomes
By Jit 2895 days agojournal.embnet.org - Next Generation Sequencing has totally changed genomics: we are able to produce huge amounts of data at an incredibly low cost compared to Sanger sequencing. Despite this, some old problems have become even more difficult, de novo assembly being on...proovread : large-scale high-accuracy PacBio correction through iterative short read consensus
By Jit 2514 days agogithub.com - proovread : large-scale high-accuracy PacBio correction through iterative short read consensus outperforms PacBioToCA/LSC in terms of accuracy and contiguity/sensitivity (http://dx.doi.org/10.1093/bioinformatics/btu392) is easy to...Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Rahul Nayak 2566 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 2546 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 2391 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...BamView: a free interactive display of read alignments in BAM data files
By Neel 2205 days agobamview.sourceforge.net - To run the application on UNIX from the downloaded jar file run the UNIX: java -mx512m -jar BamView.jar and extra command line options are given when '-h' is used: java -jar BamView.jar -h BAM files can be specified on the command line with the...ZENBU: a collaborative, omics data integration and interactive visualization system
By BioJoker 2149 days agofantom.gsc.riken.jp - ZENBU is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for novel data exploration through "on-demand" data...heatmaply: popular graphical method for visualizing high-dimensional data
By Neel 1777 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...Juicebox: Visualization and analysis software for Hi-C data
By Jit 1737 days agogithub.com - Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web. Detailed documentation is...Useful links to therapy, disease, drug and drug-target network data:
By Jit 1635 days agoUseful resources to therapy, disease, drug and drug-target network data
