BOL

Removing contaminated sequences using NCBI quality assurance tools

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...

P-value is often discussed when dealing with science. Especially in scientific journals, you will surely find mentions of the p-value. But what is it, really? Well, if I were to explain it in very simple and concise terms, I would say:“Imagine...

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...

Here is a list of mosquito species known for transmitting the Dengue virus along with essential and applied information about each species:

Cost-effective whole human genome sequencing has revolutionized the landscape of genetic research and personalized medicine by making comprehensive genetic analysis accessible to a wider population. Through advancements in sequencing technologies,...

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 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...

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) 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 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 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,...

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...

bacLIFE is a streamlined computational workflow that annotates bacterial genomes and performs large-scale comparative genomics to predict bacterial lifestyles and to pinpoint candidate genes, denominated lifestyle-associated genes (LAGs), and...

UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches,...

doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal...