BOL

github.com - PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use reciprocal best hits (RBHs) which depends...

www.genomicus.bio.ens.psl.eu - Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. Once a query gene has been entered, it...

bactopia.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...

musket.sourceforge.net - Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage...

bioinfologics.github.io - What is a k-mer anyway? A k-mer is just a sequence of k characters in a string (or nucleotides in a DNA sequence). Now, it is important to remember that to get all k-mers from a sequence you need to get...

github.com - KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per...

github.com - MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to...

www.ncbi.nlm.nih.gov - A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or...

talgalili.github.io - This work is based on ggplot2 and plotly.js engine. It produces similar heatmaps as d3heatmap, with the advantage of speed (plotly.js is able to handle larger size matrix), and the ability to zoom from the dendrogram. heatmaply also provides an...

Huge amounts of genotype data are being produced with recent technological advances, both from increasingly comprehensive and inexpensive genome-wide SNP microarrays and from ever more accessible whole-genome and whole-exome sequencing methods