GenoMiner
|
Application data |
|
| Biological application domain(s) | Sequence assembly, Sequence assembly (de novo assembly), ChIP-seq, RNA-Seq |
|---|---|
| Principal bioinformatics method(s) | Sequence assembly, Plotting and rendering, Sequence error correction, Mutation detection, Peak calling, Gene expression profiling, Sequence alignment |
| Technology | Any |
| Created at | Astrid Research, Inc. |
| Maintained? | Yes |
| Software features | GenoMiner provide workflows for Reference assembly, De novo assembly, ChIPSeq, RNASeq and more. You upload your files at the beginning, and you get the results at the end, while you can choose from various tools to use for analysis. |
| Programming language(s) | Java |
| Licence | Commercial |
| Operating system(s) | Linux |
Summary: A proprietary NGS analysis solution. Powerful hardware comes with preinstalled software, organized in workflows.
"Error: no local variable "counter" was set." is not a number.
Contents
Description
GenoMiner offers a world of NGS data analysis possibilities on a single computing platform through different workflows.
Reference assembly
Currently whole-genome and targeted re-sequencing are the most popular NGS applications. In this workflow several tools are implemented to provide the best result for your re-sequencing project including read indexing and genome indexing algorithms, specialized assemblers for Roche 454, Illumina and ABI SOLiD platforms - including our proprietary color space assembler.
De novo assembly
De novo assembly is used in case of completely unknown sequences. Without a reference sequence, you can count on millions of overlapping reads from NGS machines. The most developed de novo algorithms available today are included in the workflow to guarantee the success of your de novo sequencing projects.
Hybrid reference assembly
A hybrid reference assembly workflow is used to assure the accurate alignment to the reference of the outputs for different sequencing platforms and to manage the joint result. Similarly to the standard reference assembly workflow, the alignment process involves the most suitable tools for the different datasets. The generated result files will be merged into a single BAM file.
Hybrid de novo assembly
Most de novo sequencing projects combine the use of two or more different sequencing platforms (eg. long reads for a confident backbone and short reads for a high coverage). The aim of the hybrid de novo assembly workflow is to build up a genome or its parts by combining short/long and color coded/nucleotide coded reads. Unlike hybrid reference assembly, the read files produced by different sequencing technologies are assembled together as a joint set of mixed reads. Short reads can be single end, mate paired or paired end.
ChIP-seq
ChIP-seq is used to analyze the protein interactions with the DNA. It combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the loci on the DNA that are associated with the protein of interest. The workflow can be used to determine the protein binding/histone modification sites from the distribution of NGS reads along the reference sequence with the help of complex algorithms that use specialized mathematical methods to identify significant read densities.
BLAST
BLAST is the most frequently used tool to learn more about the similarity between the query sequence and the sequences stored in the selected database. BLAST has different variations according to the different sequence comparison methods. We have extended BLAST to enable comparison to any custom databases.
RNA-Seq
RNA-Seq or Whole Transcriptome Shotgun Sequencing is a technology to sequence cDNA in order to get information about a sample's RNA content. Depending on the method applied it can be used for the composition of the transcriptome, the varieties between different samples, quantitative information of the gene expression and regulation, etc. A complete workflow consisting of several RNA-Seq specific tools guides you through from mRNA sequencing data to expression profiles, list of differentially expressed genes, alternate splice variants etc.
Copy Number Variation (CNV)
The workflow enables genome-wide identifications of copy number variations. After mapping the sequencer reads from the study and the control samples, CNV tools analyze read distributions comparatively by utilizing complex statistical methods, detecting and indicating genomic locations where the read densities are significantly different.
Multiple Sequence Alignment
Multiple Sequence Alignment is for arranging different sequences to find similarities and differences between them. The sequences can be extremely long (like a whole genome), differ in length, contain several differences, insertions, deletions, variants relative to another sequence. It is therefore a challenging task to compare two or more sequences. The MSA workflow enables the alignment of all the sequences in a given query set to ensure the identification of conserved sequence regions or to aid in establishing evolutionary relationships by constructing phylogenetic trees, to conclude to protein functions and structures with the help of known protein domains, and many more applications.
miRNA-Seq
One of the hottest topics of biological researches today is miRNA analysis. The concept for the miRNA-Seq is basically the same as for the conventional RNA-Seq: align the reads and establish quantitative profile from the alignment. The difference is made by the specific algorithms that are suited for the process and alignment of the extremely short miRNAs., These are usually shorter than the minimum length of a single short read, so the reads contain adapters.The alignment of that short sequences requires extraordinary accuracy and confidence for a reliable result.
Links
References
none specified
To add a reference for GenoMiner, enter the PubMed ID in the field below and click 'Add'.
Search for "GenoMiner" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
