SoftGenetics - Software PowerTools for Genetic Analysis
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Software PowerTools for Genetic Analysis

SoftGenetics is the leading provider of effective, biologist friendly, easy-to-use genetic analysis software tools designed to meet the ever changing needs of today's genetic researcher and diagnostician. We offer leading edge software powertools for genetic analysis, such as Mutation Surveyor® DNA variant analysis of Sanger Sequencing software, NextGENe® 2nd Generation Sequence Analysis software, Geneticist Assistant NGS Interpretative Workbench, GeneMarker® the “Biologist Friendly” Genotyping software, GeneMarker®HID STR Human Identity software, ChimerMarker® Automated Chimerism Analysis software, and JelMarker™ Image Reading and Conversion software.



MaSTR™ Enlightened Probabilistic Mixture Analysis Software. MaSTR software features a rapid and transparent approach to Probabilistic Mixture Analysis which utilizes your forensic acumen in an easy-to-use Windows® environment for research, validation and casework applications. Server based MaSTR software is very cost effective, includes two simultaneous user licenses, and automatic queuing of multiple analyses.


GeneMarker®HTS (High Throughput Sequencing) mtDNA Analysis Software for Next Generation Sequencing Data. GeneMarker®HTS software provides a streamlined workflow for forensic and medical research mitochondrial DNA data analysis from massively parallel sequencing (MPS) systems such as the Illumina® and Ion Torrent® platforms; in an easy to use Windows® operating system. Developed in collaboration with leading laboratories, GeneMarkerHTS software provides rapid analysis of multiple samples using consensus alignment or a unique motif alignment technology spanning the origin. Analysis results include: Consensus sequence, Variants, SNPs, Indels depth of coverage graphic, consensus sequence aligned to reference (IUPAC nomenclature), read pile-up (with depth and direction indicators). Exports include a variety of reports; consensus sequence, variant reports – SNPs , insertions and deletions, haplotype, heteroplasmy, report compatible for import to EMPOP (EDNAP mtDNA Population Database). The software includes audit trail, user management, customize viewing and reporting to protect privacy of potential health information (PHI) sequences. The initial release of GeneMarkerHTS provides rapid analysis, comparisons and reporting for forensic mtDNA NextGeneration data from Illumina and Ion Torrent platforms. Subsequent releases will include STR, SNP and mixture analysis.


Mutation Surveyor® DNA variant analysis of Sanger Sequencing software…is a DNA Sequencing analysis software capable of performing variant analysis of up to 2000 Sanger sequencing files (.ab1,.RSD,.ESD & .scf) generated by Applied Biosystems Genetic Analyzers, MegaBACE as well as Beckman CEQ electrophoresis systems in 15 minutes. Utilizing patented anti-correlation technology Mutation Surveyor delivers excellent accuracy, sensitivity, low false positive and negative rates in the analysis of DNA variants: SNPS, insertions and deletions (Indels), Somatic Mutations in direct sequencing, medical sequencing, PCR sequencing, mitochondrial sequencing, and resequencing projects. The software also provides superior basecalling; correcting N-calls of the KB Basecaller or Variant Reporter® software packages; sequence alignment and reference assembly, replacing such programs as DNAStar and Sequencher or SeqPilot. The package includes a new variant knowledge database, which allows users to track variants by chromosomal position, indicate false-positives and other artifacts, and query mutation database information from popular variant databases such as dbSNP, dbNSFP, and COSMIC; automated download of annotated GenBank files including amino acid sequence; deconvolution of heterozygous indels; DNA methylation detection, mitochondrial DNA sequence analysis and quantification; customizable DNA variant coding; and reporting. Mutation Surveyor has been validated for use in clinical applications by laboratories worldwide.


NextGENe® is the perfect analytical partner for the analysis of desktop sequencing data generated by the ION PGM™, Illumina MiSeq, Roche Junior as well as higher throughput systems as the Illumina® GA and HiSeq, Ion Proton™, Roche GS and Applied BioSystems SOLiD™ systems. NextGENe software provides a biologist-friendly point & click interface, does not require scripting or other bioinformatics support. This removes the complexity often found in such programs from CLC Bio, LaserGene, DNASTAR, or open source programs such as, 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 resequencing and amplicon analysis and Structural Variant Detection; Whole Genome Alignment; Prediction and Rare Disease Discovery; Copy Number Variation (CNV); RNA-Seq and Alternative Splicing; small RNA and ChIP-Seq Expression Analysis; Metagenomics; de novo assembly.


Developed in collaboration with the Laboratory Medicine, Information Technology and Health Science Research departments of Mayo Clinic 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 conservation scores data from PhyloP, GERP++ and SiPh. Additionally, information from proprietary custom databases and from the COSMIC database of somatic mutations are easily imported into the workbench.


GeneMarker® 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 or MRC Holland's Coffalyser.Net Software. Compatible with outputs from all major sequencing systems i.e. ABI Prism®, Beckman CEQ and MegaBACE® platforms the software's Windows® based operation (XP, Vista, 7 or 8) simplifies such applications as Amplified Fragment Length Analysis (AFLP®), t-RFLP, SSR (short sequence repeat) and Microsatellite Analysis, any genotyping application. GeneMarker includes integrated modules for MLPA®, MS-MLPA, Fragile X, LOH, SNapShot®, SNPlex®, SNPWave®. TILLING® (Targeted Induced Local Lesions in Genomes), Microsatellite Instability (MSI), Haplotype Analysis, Trisomy, as well as Cystic Fibrosis Analysis utilizing chemistries from GeneProbe®, MRC Holland, Abbott Diagnostics and others. 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.


GeneMarker MTP provides the analysis power of six GeneMarker programs; reducing costs while increasing efficiency of DNA fragment analysis. The automated import and assignment of analysis parameters (templates) is intuitive, reducing complexity and analysis time. GeneMarker MTP maximizes the utility of a CE plate - include up to 6 different chemistries on the same plate. GM-MTP is rapid - processing six 96 well CE plates in approximately 30 seconds. Linked post-genotyping applications include: MLPA®, Trisomy/Aneuploidy, Cystic Fibrosis, Fragile X. LOH, MSI, STR Haplotype, ARMS®, SNaPShot® SNPs, AFLP, T-RFLP, Dendrogram Cluster Analysis, Relationship Testing, Database search, TILLING®, microsatellite analysis. GM-MTP is compatible with custom and commercial chemistries, and all major capillary electrophoresis platforms (ABI®PRISM, Beckman-Coulter®, and MegaBACE®).


NDIS Approved Expert System!

GeneMarker® HID human identity software is an excellent choice for all forensic profiling applications. This expert system software can be employed as a "biologist-friendly" replacement for GeneScan®/GenoTyper® or as an alternative to GeneMapper® ID and GeneMapper® IDX human identification software, reducing analyst required edits by 18-73% per sample. GeneMarker® HID is concordant with GeneMapper®ID and GeneMapper®IDX and compatible with ABI®PRISM 310, 3100, 3130, 3730, 3500 CE output (.fsa, .hid) and chemistries (including GlobalFiler™ 6-Dye™, Identifiler®, Minifiler®, PowerPlex®16, PowerPlex®ESI, PowerPlex®Fusion 5 and 6 Dye, Investigator®24Plex, Investigator®DIPplex and SureID® STR chemistries) uses advanced Windows® technology that is intuitive and easy to learn. In addition to standard STR analysis, GeneMarker HID software has been optimized to analyze profiles from YSTRs, Low Copy Number LCN samples, ABI's MiniFiler™ Kit, and replicate sample consensus. GeneMarker HID software includes applications to assist experts with Mixture Analysis. Relationship testing and database searching for matching/near matching profiles and familial search capabilities, which are essential for crime scene investigation, missing persons identification and paternity testing. GeneMarker HID software has been validated by forensic labs world-wide and has many time-saving tools, including an automated contamination check, to reduce casework backlogs and analyst fatigue.


Developed in collaboration with Mitchell Holland, Ph.D., Director of The Pennsylvania State University's Forensic Science Program. Review Dr. Holland's GeneMarkerHID Poster and Journal of Forensic Science article.


Reduce analysis time by up to 40% with GeneMarkerHID! (click here to read the article)


ChimerMarker®, automated chimerism analysis software, integrates speed and accuracy with a biologist-friendly interface. The software, developed in collaboration with Dr. Don Kristt, can be used to monitor chimerism level in both allogeneic 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, easily appends for longitudinal monitoring post-BMT, and has multi-lineage capabilities for chimerism analysis of T-cells, B-cells, and other cell type populations. ChimerMarker includes functions for comparison of samples at different time points to conduct longitudinal studies for monitoring each individual and a comprehensive chimerism analysis report. The chimerism analysis performs repetitive calculations (using published methods. Dr. Don Kristt). ChimerMarker also has a linked maternal cell contamination (MCC) application. ChimerMarker is compatible with ABI®PRISM, Beckman-CEQ™, and MegaBACE® genetic analyzers, and custom primers or commercially available human identification chemistries for STR genotyping (including Identifiler®, PowerPlex®16, PowerPlex®ESI). Chimerism analysis is completely linked to the main analysis screen, removing the error-prone step of data transfer from genotyping software to chimerism analysis software.


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 Image Station 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 - Software PowerTools for Genetic Analysis

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