Next Generation Sequencing (NGS)
https://en.wikipedia.org/wiki/Sequencing
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Bacterial genome assembly !!
By Jit 2902 days agobioinformatics.uconn.edu - This tutorial will serve as an example of how to use free and open-source genome assembly and secondary scaffolding tools to generate high quality assemblies of bacterial sequence data. The bacterial sample used in this tutorial will be...WEGO : simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation...
By BioStar 1828 days agowego.genomics.org.cn - WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. As the GO vocabulary became more and more popular, WEGO was widely adopted and used in many...Want to Know which genome assembler rule the world ?
Started by Rahul Agarwal 4264 days ago Replies (3) Last reply by Rahul Nayak 2295 days agoAssemblathon 2: evaluating de novo methods of genome...Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole...
By Jit 2666 days agoncbi.github.io - Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
By Seema Singh 2542 days agogithub.com - ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper...Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 1749 days agogithub.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...Largest Genome Sequenced
By Rahul Agarwal 4042 days agowww.news.ucdavis.edu - The enormous size of the loblolly pine genome having 22 billion base pairs compared to only 3 billion in the human genome. In other words, it is seven times larger than a human’s and also the largest and the most...Latest paper on comparison of mapping tools
By Rahul Agarwal 4241 days ago Comments (1)www.biomedcentral.com - A. Hatem, D. Bozdag, A. E. Toland, U. V. Catalyurek "Benchmarking short sequence mapping tools" BMC Bioinformatics, 14(1):184, 2013. http://bmi.osu.edu/hpc/software/benchmark/ http://bmi.osu.edu/hpc/software/pmap/pmap.html Other similiar...Is reference genome necessary for gene expression study in transcriptome sequencing or for variant...
Started by Rahul Agarwal 4289 days agoLike in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete de novo assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 2665 days agogithub.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in...
