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Our laboratory has developed a suite of a software for analyzing data from all commonly used next-generartion sequencing (NGS) platforms. If you are interested in using them, please email one of the authors for access.

Tool and pipeline launcher

GKNO is a tool and pipeline management system that can be used to effectively deploy the majority of tools developed in the MarthLab as well as other third-party tools. Pipelines (a defined workflow of different tasks) are easily configurable in the system. Our experience in major projects has allowed the inclusion of battle-tested pipelines with well-calibrated parameters that are available for immediate use.

The accompanying website ( includes information, discussions and tutorials on how to work with GKNO and get the best out of the system.

Contact Alistair Ward for more details.

Read Alignment and Assembly

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT.

SCISSORS is a split-read aligner that maps orphaned read mates (i.e. where one end-mate is aligned with high mapping quality, but the other mate is unmapped), as well as re-maps severely clipped reads (reads mapped with many unaligned or “clipped-off” bases). SCISSORS works with standard file formats, BAM in/out.

Sequence Alignment Utilities

BamTools BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. The accompanying paper was published in Bioinformatics.

SSW is a fast implementation of the Smith-Waterman algorithm whose API that can be flexibly used by programs written in C, C++ and other languages. For more information, see here.

Polymorphism Discovery

FreeBayes is a population-based short polymorphism detector which features support for the simultaneous detection of SNPs, INDELs, and multi-base mismatches, poly-allelic sites, polyploidy, and sample and region-specific copy number modeling. FreeBayes works with standard file formats (BAM and VCF) and easily be integrated into existing next-generation sequencing pipelines. FreeBayes is provided under a liberal MIT open source license. Users may track development via the FreeBayes public source repository.

RUFUS is a reference free approach for mutation detection that directly compares raw sequence data from two or more samples, and identifies groups of reads that are unique to a sample. The method is particularly attractive for users working with organisms that have no reference genome. The software implementation is under active development, but contact Andrew Farrell for more details.

Structural Variant (SV) Detection

Tangram is a command line toolbox for structural variation(SV) detection based on MOSAIK alignments. You can get more detailed information here.


Scotty is a tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims. The source code can be viewed here. The paper was published in Bioinformatics.

Assembly Viewing and Annotation

Gambit is a new cross-platform GUI (graphical user interface) application for sequence visualization and analysis.

Note: EagleView should be considered deprecated and is no longer supported.