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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (200 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (656 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (817 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 (870 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Programming for Lovers !
By BioStar 414 days agoprogrammingforlovers.com - Programming for Lovers (P4❤️) is a free online course that teaches programming using the Go programming language by immersing learners in fun scientific applications. Each chapter focuses on a single scientific problem and contains a core text...Creating Genetic Maps from GBS data
By BioStar 474 days agobioinformaticsworkbook.org - Genetic map, as the name suggest is simply knowing the relative positions of specific sequences across the genome. There are various methods to generate them, but most popular method is to use a cross between the known parents and examining their...PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data
By Abhi 477 days agogithub.com - Phylogenomic Analysis Pipeline for Herbarium Specimens What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies,...MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
By Abhi 477 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 484 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 499 days agopractical-stats-med-r.netlify.app - https://practical-stats-med-r.netlify.app/Metabuli 분리 improves metagenomic read classification
By Abhi 571 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 571 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 584 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 585 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,...
