SplazerS 1.1 – Detect Genomic Indel Variants with exact Breakpoints in Single- and Paired-end Sequencing

SplazerS 1.1

:: DESCRIPTION

SplazerS (Split Read Mapping as a branch of RazerS) is a tool for mapping reads containing structural variants, implemented in the highly efficient SeqAn C++ software library. SplazerS employs “split” read mapping, where prefix and suffix match of a read may be interrupted by a longer gap. This split read mapping is useful in the context of mRNA sequencing, where introns cause so-called junction reads that span exon-exon boundaries, or for the detection of small to medium-sized insertions and deletions in genomic data.

::DEVELOPER

Anne-Katrin Emde, David Weese, Marcel Schulz, Stefan Haas, and Knut Reinert

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac / Windows

:: DOWNLOAD

SplazerS

:: MORE INFORMATION

Citation

Anne-Katrin Emde et al.
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS
Bioinformatics (2012) 28 (5): 619-627.

SEWAL 20100804 – Next Generation DNA Sequencing Analysis and Visualization

SEWAL 20100804

:: DESCRIPTION

SEWAL (Sequence Evolution With Adaptive Landscapes) is an open source tools for next generation DNA sequencing analysis and visualization. SEWAL provides a new platform for DNA sequence analysis and visualization of large data sets generated by massive sequencing to perform functional in vitro genetics. The visualization incorporates the underlying LSH information in a visually intuitive manner to generate mutant spectra. When the differences in these plots resulting from altered selective pressures are visualized, they can represent projections of the hyperdimensional fitness landscape, if the frequency of the sequences has been demonstrated to correlate with phenotypic fitness

::DEVELOPER

Pitt (jpitt@fhcrc.org), Rajapakse, and Ferre-D’Amare HHMI FHCRC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX

:: DOWNLOAD

SEWAL

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Dec;38(22):7908-15. Epub 2010 Aug 6.
SEWAL: an open-source platform for next-generation sequence analysis and visualization.
Pitt JN, Rajapakse I, Ferré-D’Amaré AR.

RADtools 1.2.4 – Software for Restriction site Associated DNA Sequencing

RADtools 1.2.4

:: DESCRIPTION

RADtools is the software for processing RAD (Restriction site Associated DNA)Sequencing data. The software is a pipeline for transforming Illumina reads into candidate genetic markers.

DEVELOPER

John Davey

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Perl

:: DOWNLOAD

RADtools

:: MORE INFORMATION

Trace Recalling 0.5 – Deconvolute Double Traces Resulted from Simultaneously Sequencing Two DNA Templates

Trace Recalling 0.5

:: DESCRIPTION

Trace Recalling is a novel method for deconvoluting double traces that result from simultaneously sequencing two DNA templates. Trace Recalling identifies up to two bases at each position of such a trace. The resulting ambiguity sequence is aligned to the genome, identifying one template sequence. A second template sequence is then inferred from this alignment. This technique makes possible many exciting biological applications.

::DEVELOPER

The Brent Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Trace Recalling

:: MORE INFORMATION

Citation

Tenney A.E., Wu J.Q., Langton L., Klueh P., Quatrano R., Brent M.R.. 2007.
“A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices.”
Genome Research 17(2):212-218.

ReadSim 0.12 – Simulator for Sanger and 454 Sequencing

ReadSim 0.12

:: DESCRIPTION

ReadSim is a sequencing simulator that simulates the sequencing of reads both for Sanger and pyro-sequencing, optionally involving mate-pairs.

::DEVELOPER

Darwin Rocks Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
Java

:: DOWNLOAD

ReadSim

:: MORE INFORMATION

ReadSim is no longer maintained. All concepts of ReadSim are integrated into our new software MetaSim.