Jit
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Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
By Neel 1532 days agogithub.com - Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the...TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes
By LEGE 484 days agotritexassembly.bitbucket.io - This is the documentation of TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes. It was developed in the research group Domestication Genomics at the Leibniz Institute of Plant Genetics and Crop Research (IPK)...REAPR: a universal tool for genome assembly evaluation
By Jitendra Prajapati 3720 days ago Comments (1)genomebiology.biomedcentral.com - REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and...NGS teaching material
By Jit 3356 days agomarinetics.org - High throughput sequencing (HTS) technologies are being applied to a wide range of important topics in biology. However, the analyses of non-model organisms, for which little previous sequence information is available, pose specific problems. This...HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution
By Jit 3048 days agogithub.com - Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://genome.cshlp.org/content/27/5/747.full An ipython notebook to...EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
By Rahul Nayak 2958 days agoarthropods.eugenes.org - EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University,...SPADes team announce new version SPADes v3.15
By BioStar 1975 days agoNew SPAdes 3.15.0.0. announced by the SPADes teamMetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly
By Abhi 735 days agometagraph.ethz.ch - The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle,...Public Databases for Bioinformatics !
By Jit 1908 days agomitra.stanford.edu - https://www.nature.com/articles/s41467-020-17155-yServer Infrastructure: File Server: dhara: Synology 3614 Storage Appliance 4 Core Xeon 108TB disk storage 10Gb ethernet to SCG3 Access atx: dhara:5000 Has btsync server (try it - its much...Genomicus: genome browser that enables users to navigate in genomes in several dimensions
By Jit 3129 days agogenomicus.biologie.ens.fr - Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. Once a query gene has been entered, it...
