Results for "Bioinformatics"
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First step: Install & load “VennDiagram” package. # install.packages('VennDiagram') library(VennDiagram) Second step: Load data Add filepath if “catdoge.csv” is not in working-directory. d <- read.csv("catdoge.csv")Tags: Bioinformatics, Computational Biology, R, VennDiagram, Plot, R
2924 days ago
- Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods. This framework is comprehensive, and integrates read quality, mate pair orientation and inse...
Tags: Bioinformatics, FASTQ, NGS, ALE, Framework, Stats, Reads, Evaluation, Quality, Assembly
2924 days ago
HOMER: Software for motif discovery and next-gen sequencing analysis
This tutorial covers topics independently of HOMER, and represents knowledge which is important to know before diving head first into more advanced analysis tools such as HOMER. Setting up your computing environment Retrieving and storing sequencing files (your own data or from public so...Tags: Bioinformatics, NGS, Motif, Tutorial
2924 days ago
mrFAST: Micro Read Fast Alignment Search Tool
mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes ...Tags: Bioinformatics, FASTQ, Reads, NGS, Mapping, Alignment, Reference
2924 days ago
CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered. Canu is a hierachical assembly pipeline which runs in fo...Tags: Bioinformatics, FASTQ, NGS, Assembly, Genome, CANU, Assembler, Tool, Software
2907 days ago
MEDEA: Comparative Genomic Visualization with Adobe Flash
As the number of sequence and annotated genomes grows larger, the need to understand, compare, and contrast the data becomes increasingly important. Using the power of the human visual system to detect trends and spot outliers is necessary in such large and complex data sets. More at http:/...Tags: Bioinformatics, NGS, Visualization, Chromosome, Comparative genomics
2924 days ago
Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences
Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For visualisation, Smash outputs a SVG image, with an ...Tags: Bioinformatics, Visualization, Alignment, Free, NGS, Comparative Genomics
2924 days ago
RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes
The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently...Tags: Bioinformatics, NGS, Tk, Pipeline, Annotation, Tool, RASTtk
2923 days ago
GATB : Genome Analysis Toolbox with de-Bruijn graph
The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organis...Tags: Bioinformatics, NGS, Assembly, Tools, Tutorial, Toolbox
2922 days ago
- segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to map primer- or polyadenylation conta...
Tags: Bioinformatics, FASTQ, Reads, Map, Mapping, Segemehl, NGS
2910 days ago
