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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (199 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 (869 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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YAMP: Yet Another Metagenomic Pipeline
By BioStar 172 days agogithub.com - YAMP is constructed on Nextflow, a framework based on the dataflow programming model, which allows writing workflows that are highly parallel, easily portable (including on distributed systems), and very flexible and customisable,...sourmash: Quickly search, compare, and analyze genomic and metagenomic data sets.
By BioStar 172 days agogithub.com - sourmash is a k-mer analysis multitool, and we aim to provide stable, robust programmatic and command-line APIs for a variety of sequence comparisons. Some of our special sauce includes: FracMinHash sketching, which enables accurate...Lorikeet: Strain resolver for metagenomics
By BioStar 172 days agogithub.com - Lorikeet is a within-species variant analysis pipeline for metagenomic communities that utilizes both long and short reads. Lorikeet utilizes a re-implementaion of the GATK HaplotypeCaller algorithm, performing local re-assembly of potentially...DRAM: Distilled and Refined Annotation of Metabolism
By BioStar 172 days agogithub.com - DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs. DRAM annotates MAGs and viral contigs using KEGG (if provided by the...BioKit: a set of tools dedicated to bioinformatics, data visualisation
By Neel 190 days agobiokit.readthedocs.io - BioKit is a set of tools dedicated to bioinformatics, data visualisation (biokit.viz), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis...Panacus : A Counting Tool for Pangenome Graphs
By Neel 194 days agogithub.com - panacus is a tool for calculating statistics for GFA files. It supports GFA files with P and W lines, but requires that the graph is blunt, i.e., nodes do not overlap and consequently, each link (L) points...SeqCAT: Sequence Conversion and Analysis Toolbox
By Neel 194 days agomtb.bioinf.med.uni-goettingen.de - Your all-in-one solution for smooth conversion of sequence coordinates. Designed for bioinformatics data analysis and daily laboratory work, SeqCAT simplifies sequence coordinate conversion. Extract gene and transcript information, manipulate...Bactopia: a flexible pipeline for complete analysis of bacterial genomes
By Abhi 199 days agobactopia.github.io - Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is process your data with a broad set of tools, so that you can get to the fun part of analyses quicker! Bactopia was inspired by Staphopia, a...MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly
By Abhi 199 days agometagraph.ethz.ch - The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle,...Fundamentals of Data Visualization by Claus O. Wilke
By Abhi 199 days agoclauswilke.com - The book is meant as a guide to making visualizations that accurately reflect the data, tell a story, and look professional. It has grown out of my experience of working with students and postdocs in my laboratory on thousands of data...
