karyoploteR: plot whole genomes with arbitrary data
karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR is to offer the user an easy way to plot data a...Tags: karyoploteR, plot, whole, genomes, NGS, arbitrary, data, karyotype
1960 days ago
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq dataAfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq fi...Tags: Automatic, Filtering, Trimming, Error, Removing, Quality, Control, fastq, data
2375 days ago
poRe: an R package for the visualization and analysis of nanopore sequencing data
Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a s...Tags: poRe, R, package, visualization, analysis, nanopore, sequencing, data
2364 days ago
RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
RITA is a standalone software package and Web server for taxonomic assignment of metagenomic sequence reads. By combining homology predictions from BLAST or UBLAST with compositional classifications from a Naive Bayes classifier, RITA is able to achieve very high accuracy on short reads. Unlike o...Tags: Rapid, identification, high-confidence, taxonomic, assignments, metagenomic, data, RITA
2361 days ago
Scripts for the analysis of HGT in genome sequence data.
Scripts for the analysis of HGT in genome sequence dataTags: scripts, analysis, HGT, genome, sequence, data
2358 days ago
MinION_GC: An R script to do some QC on MinION data
Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out there: it takes about a minute to analyse a 4GB flo...Tags: MinION_GC, R, script, QC, MinION, data
2354 days ago
GPOPSIM: a simulation tool for whole-genome genetic data
GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can simulate multiple genetically correlated traits with ...Tags: GPOPSIM, simulation, tool, whole-genome, genetic, data
2310 days ago
Tags: BioCircos.js, open, source, interactive, Javascript, library, interactive, display, biological, data, web
2307 days ago
Tags: Heap, sensitive, accurate, SNP, detection, tool, low-coverage, high-throughput, sequencing, data
2218 days ago
MIX: Combining multiple assemblies from NGS data
Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent ...Tags: MIX, Combining, multiple, assemblies, NGS, data, Tools
2199 days ago