Rahul Nayak
A Bioinformatician
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Genome Annotation Transfer Utility (GATU)
By Jit 3205 days agovirology.uvic.ca - Genome Annotation Transfer Utility (GATU) was designed to facilitate quick, efficient annotation of similar genomes using genomes that have already been annotated. For example, whenever a new strain of SARS coronavirus is sequenced, it is possible,...Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
By Jit 3021 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 2726 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...Earth BioGenome Project
By Jit 2873 days agoThe central goal of the Earth BioGenome Project is to understand the evolution and organization of life on our planet by sequencing and functionally annotating the genomes of 1.5 million known species of eukaryotesGMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or...
By Shruti Paniwala 2827 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...Phased Human Genome Assembly !
By Rahul Nayak 2707 days agoDiploid Assembly of a Puerto Rican Female Adds a Rich Resource to Population-Specific Reference GenomesReferee: Genome assembly quality scores
By Jit 2680 days agogwct.github.io - Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site...Genome Annotation using MAKER tutorial !
By Shruti Paniwala 2634 days agowww.biostars.org - MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite...Genome assembly forensics: finding the elusive mis-assembly
By Jit 2597 days agoamos.sourceforge.net - We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline,...gEVAL: Genome Evaluation Browser
By Jit 2455 days agogeval.sanger.ac.uk - The gEVAL Browser allows the evaluation of genome assemblies through its tools and pre-computed analyses. The strength of this browser is the ability to navigate an up to date assembly and identify problematic regions and assist in...
