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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (636 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1092 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1253 days ago): Sequencing coverage is defined as the average number of reads that covers...
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (1305 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
By Abhi 913 days agogithub.com - MitoHiFi v3.2 is a python pipeline distributed under MIT License ! MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project...MitoFinder
By Neel 920 days agogithub.com - Allio, R., Schomaker-Bastos, A., Romiguier, J., Prosdocimi, F., Nabholz, B., & Delsuc, F. (2020) Mol Ecol Resour. 20, 892-905. (publication link) Mitofinder is a pipeline to assemble mitochondrial genomes...Biostats book !
By Abhi 935 days agopractical-stats-med-r.netlify.app - https://practical-stats-med-r.netlify.app/Metabuli 분리 improves metagenomic read classification
By Abhi 1006 days agogithub.com - 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...homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes
By Abhi 1006 days agogithub.com - 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...Genome Context Viewer (GCV)
By LEGE 1019 days agogithub.com - 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...Tools for id conversion
By LEGE 1020 days agobiit.cs.ut.ee - 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,...Proksee: in-depth characterization and visualization of bacterial genomes
By LEGE 1031 days agohttps://proksee.ca/ - 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.OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes
By Abhi 1039 days agoorthovenn3.bioinfotoolkits.net - 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...JBrowse 2: a modular genome browser with views of synteny and structural variation
By Abhi 1045 days agogithub.com - 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...
