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PeGAS: A Comprehensive Bioinformatic Solution for Pathogenic Bacterial Genomic Analysis
By LEGE 399 days agogithub.com - This is PeGAS, a powerful bioinformatic tool designed for the seamless quality control, assembly, and annotation of Illumina paired-end reads specific to pathogenic bacteria. This tool integrates state-of-the-art open-source software to provide a...SVfinder: Tool for detecting genomic rearrangement form DNA-seq data
By Robert M Willioms 3216 days agogithub.com - SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.TACOA: Taxonomic classification of environmental genomic fragments using a kernelized nearest...
By Poonam Mahapatra 3064 days agowww.cebitec.uni-bielefeld.de - TACOA is a software that can accurately predict the taxonomic origin of genomic fragments from metagenomic data sets by combining the advantages of the k -NN approach with a smoothing kernel function. TACOA can be easily installed and run on a...S-plot2: creates an interactive, two-dimensional heatmap of sequences
By Jit 2929 days agobitbucket.org - S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can...Bourque Lab
The goal of the lab is to understand mammalian genomes using comparative genomic and epigenomic analyses. Areas of interest include: the evolution of regulatory sequences, the role of transposable elements in gene regulation and the impact of genome...Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
By Jit 2399 days agogithub.com - A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg) Link to working demo:...sourmash: Quickly search, compare, and analyze genomic and metagenomic data sets.
By BioStar 821 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...dna2bit: an ultra-fast and accurate genomic distance estimation software
By LEGE 400 days agogithub.com - dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. It has been thoroughly tested using the g++ and clang compilers on both Linux and...GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
By Jit 3407 days agogithub.com - GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.htmlFeatures Mapping position agnostic to alignment parameters. ...Reference-free prediction of rearrangement breakpoint reads
By Neel 3133 days agocode.google.com - lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing...
