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.
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.
MUTATION SURVEYOR APPLICATIONS
NextGENe is the perfect analytical partner for the analysis of desktop sequencing data produced by the ION PGM™, Roche Junior, Illumina MiSeq as well as high throughput systems as the Ion Torrent Proton, Roche FLX, Applied BioSystems SOLiD™ and Illumina® platforms. NextGENe software runs on a Windows® Operating System, which provides a biologist-friendly point & click interface, and does not require scripting or other bioinformatics support, often required when using programs such as CLC Bio, LaserGene, DNASTAR, MAQ,SOAP,Top Hat, BWA and Bowtie.
NextGENe software employs unique platform specific technologies in one free-standing multi -application package. NextGENe software contains analysis modules for SNP/INDEL & Structural Variant Analysis (resequencing & Amplicon analysis), Copy Number Variation (CNV), Prediction and Rare Disease Discovery; Whole Genome Alignment; Transcriptome; Alternate Splicing of Exons & Transcript Expression levels; RNA Seq; ChIP-Seq, Serial Analysis of Gene Expression (SAGE) analysis; Digital Gene Expression (DGE), Exome Assembly & Variant Discovery; miRNA Analysis & Quantification; Metagenomics; de novo assembly, CNV and Exome Capture.
NextGENe contains analysis modules for:
- SNP/INDEL Analysis
- Copy Number Variation (CNV)
- Mining for Somatic Mutations in NGS sequencing
- Prediction and Rare Disease Discovery
- Whole Genome Alignment
- Annotated Reference Genomes
- Transcriptome/RNA-SEQ: Expression and Alternative Splicing Analysis
- miRNA, Chip-Seq, Serial Analysis of Gene Expression (SAGE) & Digital Gene Expression (DGE) Analysis
- de novo assembly
- Targeted Re-Sequencing
- Forensic Profiling
- SNP & INDEL discovery with Ion Torrent PGM & Proton data
- Automation Analysis & Reporting Pipeline
- Automated, Custom reporting of Analysis and QC of NGS sequencing
- Multi-Sample Variant Comparison
- Annotation Tracks
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.
Developed in collaboration with the Laboratory Medicine, Information Technology and Health Science Research departments of Mayo Clinic, Rochester MN.
Geneticist Assistant NGS Interpretative Workbench is a web-based tool for the control, visualization, interpretation and historical knowledge base of next generation sequencing data targeted at specific genes for the purpose of identifying potentially pathogenic variants associated with specific conditions such as hereditary colon cancer. Geneticist Assistant is compatible with data processed from all leading Next Generation Sequencing platforms such as those from Ion Torrent, Illumina and Roche. The program accepts standardized BAM and VCF files, includes prediction information from SIFT, Polyphen2, LRT and Mutation Taster, as well as three conservation scores from PhyloP, GERP++ and SiPhy. Additionally, data from proprietary custom databases and information from the COSMIC database of somatic mutations are easily imported into the workbench.
Geneticist Assistant is designed to integrate multiple data sources into an efficient workflow for laboratories utilizing Next Generation Sequencing technology. The workbench comes with an array of tools to speed NGS workflows from quality control through laboratory reporting with accessibility either through encrypted internet protocol by multiple collaborating institutions or a local institutional network or through a local computer.
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.
GeneMarker® software is a unique genotype analysis software which integrates new technologies enhancing the speed, accuracy and ease of analysis.
Biologist-friendly, the software is an excellent alternative to Applied BioSystems Genotyper® and GeneScan® or GeneMapper® software; LiCor's SAGA, MegaBACE® Genetic Profiler and Fragment Profiler, SeqencePilot®, or MRC Holland's Coffalyser.Net software.
Compatible with outputs from all major sequencing systems i.e. ABI®PRISM, Beckman-Coulter®, and MegaBACE® platforms the software's Windows® based operation (XP,Vista 7 or 8) simplifies such applications as:
- Amplified Fragment Length Analysis (AFLP®)
- SSR (short sequence repeat) and Microsatellite Analysis
- Any genotyping application.
GeneMarker software includes integrated modules for:
- TILLING® (Targeted Induced Local Lesions in Genomes)
- Microsatellite Instability (MSI)
- Haplotype Analysis
- as well as Cystic Fibrosis Analysis utilizing chemistries from GeneProbe®, MRC Holland, Abbott Diagnostics and others, Fragile X from Asuragen® and custom chemistries.
Incorporated tools include:
- Kinship Analysis of Wild Populations
- Phylogeny Clustering
- Project Comparison
- as well as a User Management providing an analysis audit trail and editing.
View live webinars
- Introduction to GeneMarker software
- Creating Custom Panels
- MLPA® Analysis
- Aneuploidy/Trisomy Analysis
- Relationship Testing and Cluster Analysis
- Merging two or more multiplexes for greater resolution of dendrogram
- Fragile X Analysis Using GeneMarker software
Although GeneMarker software can be used for any genotyping application, we have incorporated preset analysis modules for many key genotyping applications.
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™ 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.
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.