Mason – JavaScript Widget for Viewing Sequence Features and Annotations

Mason

:: DESCRIPTION

Mason is a JavaScript and SVG-based viewer meant to display annotated regions or features of DNA and protein sequences.

::DEVELOPER

Mason team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JavaScript

:: DOWNLOAD

 Mason

:: MORE INFORMATION

Citation

BMC Res Notes. 2015 Dec;8(1):1009. doi: 10.1186/s13104-015-1009-z. Epub 2015 Mar 7.
Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences.
Jaschob D1, Davis TN, Riffle M.

Mason 0.1.2 – Read Simulator software for Illumina, 454 and Sanger reads

Mason 0.1.2

:: DESCRIPTION

Mason is a read simulator software for Illumina, 454 and Sanger reads. Its features include position specific error rates and base quality values. For Illumina reads, we give a comprehensive analysis with empirical data for the error and quality model. For the other technologies, we use models from the literature. It has been written with performance in mind and can sample reads from large genomes.

::DEVELOPER

Manuel Holtgrewe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX /Windows

:: DOWNLOAD

 Mason

:: MORE INFORMATION

Citation

Holtgrewe, M. (2010).
Mason – a read simulator for second generation sequencing data.
Technical Report TR-B-10-06, Institut für Mathematik und Informatik, Freie Universität Berlin.

MASon rev12 – Reduce the Computing Time of NGS Analysis Pipelines

MASon rev12

:: DESCRIPTION

MASon (Million Alignments in Seconds) is a C++ library that uses high performance architectures to reduce the computing time of NGS analysis pipelines.MASon employs an optimized SW implementation to align NGS reads and exploits graphic cards (CUDA, OpenCL) and CPU vector instructions (SSE, OpenCL). This allows computation of millions of short local pairwise sequence alignments (36bp – 1,000bp) within a few seconds. MASon can be easily integrated into NGS analysis pipelines and allows programmers to optimally utilize modern hardware, ranging from desktop computers to high-end clusters.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MASon

:: MORE INFORMATION

Citation:

Rescheneder, P., von Haeseler, A., Sedlazeck, F. J.,
Mason: Million alignments in seconds,
In Proceedings of the International Conference on Bioinformatics: Models, Methods and Algorithms, 2012, Algarve, Portugal