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• • BioStar@biostar

  

  BioStar created a page Bioinformatics tools for genome assembly ! 956 days ago

  There are numerous genome assembly tools available, each with its strengths and weaknesses. Here is a list of some widely used genome assembly tools as of my last update in September 2021: SPAdes: An assembler specifically designed for...
• • BioStar@biostar

  

  BioStar answered the question What I should focus on before applying to PhD bioinformatics positions ? 956 days ago

  Before applying to Ph.D. positions in bioinformatics, it's essential to prepare yourself thoroughly to increase your chances of success. Here are some key areas to focus on: 1. Academic Preparation: Ensure you have a strong foundation in...
• • BioStar@biostar

  

  BioStar answered the question How to create a Linux OS bootable drive ? 956 days ago

  Creating a bootable Linux OS drive involves creating a bootable installation media (such as a USB flash drive) from the Linux distribution's ISO file. The process can vary slightly depending on your operating system (Windows, macOS, or Linux). Here...
• • BioStar@biostar

  

  BioStar answered the question Should I buy chromebook for bioinformatics work ? 956 days ago

  Whether you should buy a Chromebook for bioinformatics work depends on several factors, including the specific bioinformatics tasks you need to perform, your workflow, and your overall computing needs. Chromebooks can be a cost-effective option for...
• • BioStar@biostar

  

  BioStar answered the question What are the best method to validate genome assembly ? 956 days ago

  Validating a genome assembly is crucial to ensure its accuracy and completeness. Several methods can be employed to assess the quality of a genome assembly. Here are some of the best methods commonly used in the field: Benchmarking against a...
• • BioStar@biostar

  

  BioStar published a news post NCBI Datasets pages 968 days ago

  Assembly and Genome record pages now redirect to new NCBI Datasets pages.
• • Abhi@abhinav

  

  Abhi created a new bio-script R script for Circos plot ! 969 days ago
• • Abhi@abhinav

  

  Abhi answered the question Why bioinformatics is important ? 974 days ago

  Bioinformatics is an interdisciplinary field that combines biology, computer science, statistics, and mathematics to analyze and interpret biological data. It plays a crucial role in advancing our understanding of biological processes, enabling...
• • Abhi@abhinav

  

  Abhi answered the question Do we need any ethical clearance to work in SARS-CoV2 data ? 974 days ago

  Working with SARS-CoV-2 data, especially data related to human subjects, often involves sensitive information and potential privacy concerns. The need for ethical clearance or approval depends on the specific context and the nature of the research...
• • Abhi@abhinav

  

  Abhi bookmarked Metabuli 분리 improves metagenomic read classification 1006 days ago

  Metabuli 분리 improves metagenomic read classification through metamers, DNA-AA k-mers, to be sensitive and specific, recovering 99% and 98% of DNA or AA classifiers.   Metabuli is metagenomic classifier that jointly analyze both DNA and amino...

  https://github.com/steineggerlab/Metabuli
• • Abhi@abhinav

  

  Abhi bookmarked homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes 1006 days ago

  This tutorial describes the usage of homologizer to phase gene copies into polyploid subgenomes. The tutorial is an abbreviated version of a soon-to-be published paper in Methods in Molecular Biology. Please see that paper for many more...

  https://github.com/wf8/homologizer
• • LEGE@lege

  

  LEGE bookmarked Genome Context Viewer (GCV) 1019 days ago

  The Genome Context Viewer (GCV) is a web-app that visualizes genomic context data provided by third party services. Specifically, it uses functional annotations as a unit of search and comparison. By adopting a common set of annotations, data-store...

  https://github.com/legumeinfo/gcv
• • LEGE@lege

  

  LEGE bookmarked Tools for id conversion 1020 days ago

  g:Convert enables to convert between various gene, protein, microarray probe and numerous other types of namespaces. We provide at least 40 types of IDs for more than 60 species. The 98 different namespaces supported for human include Ensembl,...

  https://biit.cs.ut.ee/gprofiler/convert
• • LEGE@lege

  

  LEGE bookmarked Proksee: in-depth characterization and visualization of bacterial genomes 1031 days ago

  Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file.

  https://proksee.ca/
• • LEGE@lege

  

  LEGE posted to the wire 1033 days ago

  https://hplgit.github.io/bioinf-py/doc/pub/html/main_bioinf.html #Learn #Python #Bioinformatics
• • Abhi@abhinav

  

  Abhi bookmarked OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes 1039 days ago

  OrthoVenn3 is a powerful tool for comparative genomics analysis, used as a web server for full genome comparisons, annotation, and evolutionary analysis of orthologous clusters across multiple species. It has already been used by thousands of users...

  https://orthovenn3.bioinfotoolkits.net/
• • Abhi@abhinav

  

  Abhi bookmarked JBrowse 2: a modular genome browser with views of synteny and structural variation 1045 days ago

  igvjs - a create-react-app with igv package from npm installed. the igv.js is instrumented to output "DONE" to the console when finished, and to have an increased fetchSizeLimit (which is otherwise git in CRAM longread tests) jb2-web - stock...

  https://github.com/GMOD/jb2profile
• • Abhi@abhinav

  

  Abhi posted to the wire 1045 days ago

  Nice #Upset #plot tutorial https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions
• • Abhi@abhinav

  

  Abhi bookmarked genomenotebook 1050 days ago

  https://dbikard.github.io/genomenotebook/ Install pip install genomenotebook How to use Create a simple genome browser with a search bar. The sequence appears when zooming in. import genomenotebook as gn g=gn.GenomeBrowser(genome_path,...

  https://dbikard.github.io/genomenotebook/
• • Abhi@abhinav

  

  Abhi answered the question Do we need any ethical clearance to work in SARS-CoV2 data ? 1061 days ago

  While SARS-CoV-2 data handling may not be directly associated with humans, it is important to remember that this data often includes personal and sensitive information about individuals, such as their health status, medical history, and demographic...

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