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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (639 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1096 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1257 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 (1309 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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REGEN: Ancestral Genome Reconstruction for Bacteria
By Rahul Nayak 2926 days agowww.mdpi.com - REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the...scikit-bio™ is an open-source, BSD-licensed, python package providing data structures, algorithms,...
By Jit 2930 days agohttp://scikit-bio.org/ - scikit-bio is currently in beta. We are very actively developing it, and backward-incompatible interface changes can and will arise. To avoid these types of changes being a surprise to our users, our public APIs are decorated to make it clear...An Introduction to Applied Bioinformatics
By Jit 2930 days agohttp://readiab.org/ - IAB is primarily being developed by Greg Caporaso(GitHub/Twitter: @gregcaporaso) in the Caporaso Lab at Northern Arizona University. You can find information on the courses I teach on my teaching website and...Protein Subcellular Localization Prediction
By Poonam Mahapatra 2931 days agoabi.inf.uni-tuebingen.de - Assigning subcellular localization to a protein is an important step towards elucidating its interaction partners, function, and potential role(s) in the cellular machinery. Computational tools offer an attractive complement to time-consuming and...Generate interactive codon usage plots
By Jit 2932 days agogithub.com - Generate interactive codon usage plots as used at ensembl.lepbase.org. The input file format can be generated from an Ensembl database using the export_json.pl script from the easy-import pipeline. live demoGenome assembly stats plotting
By Jit 2932 days agogithub.com - A de novo genome assembly can be summarised b y a number of metrics, including: Overall assembly length Number of scaffolds/contigs Length of longest scaffold/contig Scaffold/contig N50 and N90Assembly base composition, in...ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
By Jit 2941 days agohttp://etetoolkit.org - ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and...Tallymer: method to compute K-mer frequencies and its application to annotate large repetitive...
By Jit 2944 days agowww.zbh.uni-hamburg.de - Tallymer is based on enhanced suffix arrays. This gives a much larger flexibility concerning the choice of the k-mer size. Tallymer can process large data sizes of several billion bases. We used it in a variety of applications to study the...MeDuSa: a multi-draft based scaffolder
By Abhimanyu Singh 2946 days agogithub.com - MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa...circosJS: d3 library to build circular graphs
By Jit 2946 days agogithub.com - Circos is a javascript library to easily build interactive graphs in a circular layout. It's based on d3.js. It aims to be a javascript version of the Circos software. You should consider using Circos to show: relationships...
