swgis v2.0 : a seqword genomic island sniffer
swgis v2.0 is the modified version of the seqword genomic island sniffer. this version is specifically optimized for predicting genomic islands in eukaryotic genomes. swgis v2.0 was tested on several eukaryotic species of different lineages. all identified genomic islands were deposited in t...Tags: swgis, modified, version, seqword, genomic, island, sniffer, HGT, rna, genome
1974 days ago
pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks
pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot: bigwig bed (many options) bedgraph links (represented as arcs) Hi-C matrices (if HiCExplorer is installed)Tags: Standalone, program, library, plot, beautiful, genome, browser, tracks
1966 days ago
Tags: ASCIIGenome, genome, browser, command, line, interface, designed, running, console, terminals.
1966 days ago
ANItools web: a web tool for fast genome comparison within multiple bacterial strains
ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you could send us the genome sequence by email. Then ...Tags: ANItools, web, tool, fast, genome, comparison, multiple, bacterial, strains
1961 days ago
SKESA: strategic k-mer extension for scrupulous assemblies
SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity, handles low-level contamination in reads, is fast,...Tags: SKESA, strategic, k-mer, extension, scrupulous, assemblies, genome, assembly
1961 days ago
NovoGraph: building whole genome graphs from long-read-based de novo assemblies
NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of principle by creating a genome graph of seven ethnical...Tags: NovoGraph, building, whole, genome, graphs, long-read-based, de novo, assemblies
1960 days ago
Merqury: reference-free quality and phasing assessment for genome assemblies
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 reference. Merqury provides a set of tools for this ...Tags: Merqury, reference-free, quality, phasing, assessment, genome, assemblies
1391 days ago
Tags: Genobuntu, software, package, packages, oriented, NGS, assembly, genome
1934 days ago
genoPlotR - plot gene and genome maps project!
genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files. Features Linear representation of several segments of DNA Comp...Tags: genoPlotR, plot, gene, genome, maps, project, R
1933 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an issue for downstream analysis whether you're wor...Tags: Purge, Haplotigs, Pipeline, curate, heterozygous, diploid, genome, assemblies
1929 days ago