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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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Virus Bioinformatics Tools
By LEGE 245 days agoevirusbioinfc.notion.site - Bioinformatics tools play a crucial role in studying viruses, enabling researchers to analyze their genetic makeup, structure, function, and evolution. Here are some commonly used bioinformatics tools for virus...MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction
By Abhi 261 days agogithub.com - MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard...A web-based tool for sequence alignment statistics and innovative visualization
By BioStar 265 days agobioinformatics.um6p.ma - AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA...Minda: a tool for evaluating structural variant (SV) callers
By LEGE 269 days agogithub.com - Minda is a tool for evaluating structural variant (SV) callers that standardizes VCF records for compatibility with both germline and somatic SV callers, benchmarks against a single VCF input file, or benchmarks against an ensemble call set...Severus: a somatic structural variation (SV) caller for long reads
By LEGE 269 days agogithub.com - Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT). It is designed for matching tumor/normal analysis, supports multiple tumor samples, and produces accurate and complete somatic and germline calls. Severus...GraphPath: A graph attention model for molecular stratification with interpretability based on the...
By LEGE 272 days agogithub.com - Achieving accurate and interpretable clinical predictions requires paramount attention to thoroughly characterizing patients at both the molecular and biological pathway levels. In this paper, we present GraphPath, a biological knowledge-driven...ExRec: Exclusion of Recombined DNA
By LEGE 272 days agogithub.com - ExRec (Exclusion of Recombined DNA) is a Python pipeline that implements the four-gamete test to filter out recombined DNA sites from up to thousands of DNA sequence loci. The pipeline consists of five standalone applications: the first two convert...CGView.js is a Circular Genome Viewing tool
By LEGE 273 days agohttps://js.cgview.ca/ - CGView.js is a Circular Genome Viewing tool for visualizing and interacting with small genomes. This software is an adaptation of the Java program CGView. CGView.js is the genome viewer of Proksee, an expert system for genome...Proksee
By LEGE 273 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. Please Cite the Following Grant JR, Enns E, Marinier E,...R Package for PCA Analysis
By LEGE 275 days agorpubs.com - An R package for performing principal component analysis (PCA) of genomics data. The package performs PCA, generates the publication-ready plots, and identifies population-specific outlier individuals. The package can be accessed on...
