Jit
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Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
By Jit 2582 days agoschatzlab.cshl.edu - Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used...funannotate: Eukaryotic Genome Annotation Pipeline
By Jit 2288 days agogithub.com - Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this...SciLifeLab tutorial for bioinformatics analysis !
By Jit 2443 days agoscilifelab.github.io - SciLifeLab is a national center for molecular biosciences with focus on health and environmental research. Courses Old courses (2012-2014) Metagenomics Workshop 2015 November - Uppsala2016 November - Uppsala2017 November - Uppsala Introduction...Jvarkit : Java utilities for Bioinformatics
By Jit 2391 days agolindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for BioinformaticsBAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus
By Jit 2252 days agowww.zhanyuwang.xin - BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the...SIMBA: a Genome Assembly Project Management System
By Neel 2217 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)...gVolante: Completeness Assessment of Genome/Transcriptome Sequences
By Neel 2172 days agogvolante.riken.jp - A brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly...Caulobacter ethensis - 2.0 : Computer-generated Genome of a Living Organism
By Abhimanyu Singh 2092 days agoAll the genome sequences of organisms known throughout the world are stored in a database belonging to the National Center for Biotechnology Information in the United States. As of today, the database has an additional entry: Caulobacter...gVolante: Completeness Assessment of Genome/Transcriptome Sequences
By Jit 1966 days agogvolante.riken.jp - gVolante provides an online interface for completeness assessment of user’s original or publicly available sequence datasets as well as for browsing results of completeness assessment performed on publicly available genome and...Genome Informatics Section Lab !
Our section develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. We aim to improve such foundational processes and translate emerging...
