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GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or...
By Shruti Paniwala 2979 days agoacademic.oup.com - GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap...SIMBA: a Genome Assembly Project Management System
By Neel 2808 days agoufmg-simba.sourceforge.net - SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS)...De novo Genome Assembly for Illumina Data
By Rahul Nayak 2391 days agowww.melbournebioinformatics.org.au - Written and maintained by Simon Gladman - Melbourne Bioinformatics (formerly VLSCI) Protocol Overview / Introduction In this protocol we discuss and outline the process of de novo assembly for small to medium sized...SPADes team announce new version SPADes v3.15
By BioStar 2030 days agoNew SPAdes 3.15.0.0. announced by the SPADes teamGenome Assembly Workshop 2020
By Jit 1808 days agoucdavis-bioinformatics-training.github.io - Our team offers custom bioinformatics services to academic and private organizations. We have a strong academic background with a focus on cutting edge, open source software. We replicate standard analysis pipelines (best practices) when...NCBI Datasets pages
By BioStar 1122 days agoAssembly and Genome record pages now redirect to new NCBI Datasets pages.Step-by-Step Guide to Running Genome Assembly
By Abhi 602 days agoGenome assembly is a powerful process that transforms raw sequencing data into a coherent representation of an organism’s genome. By following this step-by-step guide, you can successfully assemble genomes and uncover valuable biological insights....ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
By Neel 2394 days agogithub.com - ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have more than 10 samples (recommended amount - 40 since we estimate variances from...kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference...
By Jit 3163 days agosourceforge.net - Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages...Platypus – R package for object detection and image segmentation.
By BioStar 2097 days agogithub.com - platypus is an R package for object detection and semantic segmentation. Currently using platypus you can perform: multi-class semantic segmentation using U-Net architecture multi-class object detection...
