SoftGenetics
Software PowerTools for Genetic Analysis
Next-gen Sequencing • Genotyping • Copy Number • Chimerism
SoftGenetics' mission is to provide researchers and clinicians with effective, biologist friendly, easy-to-use software analysis tools to meet the ever changing needs of today's genetic researcher and diagnostician. We know our success is totally dependent upon our ability to meet the evolving needs of the user community. All of our software tools are the result of close, effective collaborations with the genetic community.
Mutation Surveyor
A Unique tool for DNA Variant Analysis from Sanger Sequence Traces
Mutation Surveyor® is a DNA Sequencing software for the analysis of Sanger sequencing files (.ab1,.RSD,.ESD & .scf) generated by Applied Biosystems Genetic Analyzers, MegaBACE as well as Beckman CEQ electrophoresis systems.
Mutation Surveyor® Sequence analysis and assembly software utilizes our patent pending physical trace comparison technology which provides accuracy >99% when using bi-directional Phred 20 quality sequence traces.
The software is an excellent tool for both discovery anddiagnostic applications, and accepts sequence traces from all major sequencing systems such as those marketed by Applied BioSystems, Foster City CA, Beckman Coulter or MegaBACE systems, and is compatible with either terminator or primer chemistries. The software's unique technology provides the best tool for locating all DNA variants: Homozygote, Heterozygote, Indels and heterozygote insertions or deletions.
View the Mutation Surveyor video.
Download the 2011 Mutation Surveyor brochure.
MUTATION SURVEYOR APPLICATIONS |
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Genetic Diversity Analysis |
Hypervariable Mutation Detection |
Methylation Detection |
Sequence Assembly |
Somatic Mutation Detection |
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NextGENe
NextGENe® software has been developed specifically for use by biologists performing analysis of next generation sequencing data from Roche Genome Sequencer FLX, Illumina GA/HiSeq, Life Technologies Applied BioSystems' SOLiD™ System, PacBio and Ion Torrent PGM platforms.
NextGENe contains analysis modules for:
- SNP/INDEL & Structural Variant Analysis
- Deep Sequencing, Whole Genome Alignment
- Forensic Human Identity
- Alternate Splicing of Exons & Transcript Expression levels
- RNA Seq
- ChipSeq
- SAGE analysis
- Digital Gene Expression DGE
- Exome Assembly & Variant Discovery
- miRNA Analysis & Quantification
- Metagenomics
- de novo assembly
- Exome Capture
NextGENe's Windows® based operation removes the complexity found with programs such as CLC bio, Lasergene's SeqMan & NGEN, MAQ & SOAP, Top Hat, BWA & Bowtie. Biologists simply input the systems raw reads or SAM and BAM files, select the application and click go to perform the analysis of 2nd generation sequencing data. Upon completion results are presented in NextGENe's graphical annotated whole genome browser/viewer for review editing and commenting.
NextGENe is designed in a biologist friendly Windows® environment significantly reducing the need for additional bioinformatics resources and costs. NextGENe utilizes low cost desk 64-bit hardware configuration with a minimum of 8 GB RAM.
View the NextGENe introduction video.
ChimerMarker
ChimerMarker™ Automated Chimerism Analysis Software was designed with the haematologist & cytogeneticist in mind. 
This software eliminates the time consuming and the error-prone step of data transfer from genotyping software to chimerism analysis software, associated with using traditional methods such as FISH, fluorescent in situ hybridization and STR Profiling when performing Chimerism quantification.
ChimerMarker™ is used to monitor chimerism level in both allogeneic and autologous stem cells transplant (SCT) or hematopoietic stem cells transplant (HSCT), bone marrow transplant (BMT, post bone marrow engraftment), and cord and peripheral blood stem cells transplant (PBSCT) samples.
The program provides accurate, rapid genotyping and chimerism analysis; automatically identifies donor and recipient peaks in post-BMT samples, calculates percent chimerism and quality metrics for single donor or double donor cases, and has multi-lineage capabilities for chimerism analysis of T-cells, B-cells, and other cell type populations.
View the ChimerMarker video.
CHIMERMARKER APPLICATIONS |
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Post-transplant Sample Analysis |
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GeneMarker
GeneMarker® the "Biologist Friendly" genotyping software… is an excellent replacement for GeneScan®/GenoTyper® or an easy-to-use alternative to GeneMapper®. GeneMarker's basic operation is simple, fast and accurate. GeneMarker is compatible with all major electrophoresis systems including Applied Biosytems PRISM™ Genetic Analyzer, MegaBACE™, Beckman-Coulter and SpectruMedix systems.
When used in combination with JelMarker™ GeneMarker is an excellent choice for analysis of any gel image from systems such as the LI-Cor® 4300 DNA analyzer or Kodak Image Station 4000R.
GeneMarker HID
GeneMarker®HID STR Human Identity Software meets expert system requirements… making it an excellent replacement or alternative to GeneScan/Genotyper or GeneMapperID.
Collaborator comparison studies have indicated analysis time savings of over 40% in comparison toGeneMapperID. Developed in collaboration with the Pennsylvania State University Forensic Science program GeneMarkerHID is an excellent tool for casework, Mixture Analysis, paternity and all other human identity applications such as stem cell research and identification.
JelMarker
JelMarker™ image reading and conversion software…was developed in response to a growing demand for software that can analyze fluorescence, chemiluminescence and autoradiography gel image files - especially those from LI-COR's 4300 DNA Analyzer and KODAK's ImageStation 4000R.
JelMarker™ is a simple, stand-alone image reading software providing highly accurate lane and band recognition. Easy-to Use, modern Windows technology permits rapid point and click modification to lane and band positions.
CGH Explorer
CGH Explorer™ Comparative Genome Hybridization software… utilizes genomic DNA from both reference and test genome that are labeled with fluorescent dyes. The genomic samples competitively hybridize with an array of probes arranged on a substrate. The hybridized slide can be scanned evaluating the signal intensity ratio for the two dyes to determine the copy number for each DNA segment. The majority of microarray platforms use short DNA fragments (25- 75 base pairs), oligonucleotides, or larger BAC clones of about 100 kbp. Along with the arrays covering chromosome specific regions, there are genome wide arrays used for quick assessment of losses and gains in larger regions. In addition, cDNA arrays, originally designed for gene expression profiling, are used to evaluate the number of copies in coding regions.
CGH Explorer™ is an easy-to-use software tool for analyzing two color copy number alteration arrays from multiple platforms, including AgilentTechnologies, Illumina, AffyMetrix, NimbleGen, BioRobotics, Combimetrix and others.
The software performs raw image analysis and gridding eliminating image biases to significantly improving analysis accuracy. Simple, user-friendly interface and automation features speed analysis providing final results within a few mouse clicks.
About Softgenetics
SoftGenetics, LLC specializes in the development of genetic analysis tools for both research and diagnostic applications. Hallmarks of SoftGenetics software tools are advanced technologies, providing exceptional accuracy, and sensitivity in an easy-to use Windows® user interface.
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