Computational Genomics: Applied Comparative Genomics
...urse will focus on human genomics and human medical applications, but the techniques will be broadly appli...ysis, and cancer genomics. The grading will be based on assignments, a midterm exam, class presentations,...2413 days ago
2413 days ago
Ribbon: Visualizing complex genome alignments and structural variation:
...b on the right. Local installation: You can install Ribbon locally from Github by following the instructions here: https://github.com/MariaNattestad/Ribbon2413 days ago
phyloXML: XML for evolutionary biology and comparative genomics
...ribe phylogenetic trees (or networks) and associated data. PhyloXML provides elem...ents. Using these standardized elements allows interoperability between various a...sion of <property> elements by phyloXML, extensibility as well as domain sp...2413 days ago
PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
PLAST is a fast, accurate and NGS scalable bank-to-bank sequence s...comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture, PLAST takes full advant...est quality results, Contains a fully integrated data filtering engine c...2411 days ago
dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
dnaPipeTE (for de-novo assembly & annotation...is a pipeline designed to find, annotate and quantify Transposable Ele...y useful to quantify the proportion of TEs in newly sequenced genomes s...dnaPipeTE is developped by Clément Goubert, Laurent Modolo...2410 days ago
MinION_GC: An R script to do some QC on MinION data
...data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this app...it's a lot quicker than most other things out there: it takes about a minute to analyse a 4GB flowcell on...2409 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
Our software can be used to generate collections of synthetic reads that reflect the diverse tax...he metagenome using a simulation of a number of different sequencing technologies. A population sampl...2408 days ago
Bandage: interactive visualization of de novo genome assemblies
...can zoom in to specific areas of the graph and interact with it by moving nodes,...be performed within the Bandage graphical user interface and the hits are display...://github.com/rrwick/Bandage. Bandage is implemented in C++ and supported on Linu...2408 days ago
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
...nect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidop...measurement when compared with the contigs produced using unconnected reads.2407 days ago