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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (167 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (623 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (784 days ago): Sequencing coverage is defined as the average number of reads that covers...
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Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical...
By BioStar 1584 days agowww.sequenceontology.org - We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers...ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes
By Jit 1592 days agogithub.com - ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each ‘alien genes’ with an unusual sequence composition according to the host genome background to detect HGT events in...RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler
By LEGE 1597 days agogithub.com - RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types: single-end/paired-end bulk RNA-seq (strand-specific/agnostic) paired-end single-cell RNA-seq...MAJIQ 2 is released !
By LEGE 1597 days agomajiq.biociphers.org - Ability to detect, quantify, and visualize complex and de-novo splicing variations from RNASeq. MAJIQ’s accuracy compares favorably to other algorithms. MAJIQ 2 is *way* faster, more memory and I/O efficient New visualization (VOILA...Predict Gene Ontology with sequences !
By LEGE 1598 days agoekhidna2.biocenter.helsinki.fi - PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE) and GO...SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
By Jit 1602 days ago Comments (1)bitbucket.org - SVEngine (Structural Variants Engine) SVEngine is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios. SVEngine takes as input...merqury: Evaluate genome assemblies with k-mers
By Jit 1603 days agogithub.com - Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality...Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 1606 days agogithub.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...PhiSpy: PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes
By Jit 1606 days agogithub.com - PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes. Given an annotated genome it will use several approaches to identify the most likely prophage regions. Initial versions of PhiSpy were written by Sajia Akhter...truvari: Structural variant comparison tool for VCFs
By Jit 1606 days agogithub.com - Structural variant comparison tool for VCFs Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure. Spiral Genetics Motivation
