描述
Geneious 生物信息學軟體
Geneious Prime 產品特色
NGS Pre-Processing
- Import Illumina, PacBio and NanoPore reads
- Trim, filter and demultiplex both single-end and paired-end data
- Merge paired reads
- De-duplicate
- Error correct and normalize
- Filter out chimeras
Mapping and de novo Assembly
- Simply switch between industry leading algorithms for mapping and de novo assembly
- Support for assembly of Sanger and NGS data, including Illumina, PacBio and Oxford Nanopore reads of any length, including paired-end reads and hybrid assemblies
- Produce circular contigs when assembling microbial genomes, plasmids and other circular sequences
- Genome comparison and finishing with MAUVE genome alignment
- Mappers including Geneious, Geneious for RNA Seq, BBMap, Minimap2, Bowtie2 and TopHat
- De novo assembly algorithms including Geneious, SPAdes, Flye, MIRA, Tadpole and Velvet
Variant Calling and Expression Analysis
- Call SNPs/variants using Geneious or FreeBayes
- Perform real-time filtering of tabular results with synchronized genome view
- Calculate and compare expression levels on mapped RNA-seq data
- Visualize using PCA and volcano plots
Sequence Analysis
- Trim, assemble, and view Sanger sequencing trace files
- Correct base calls and create consensus sequences
- Annotate motifs, ORFs and repeats
- Predict genes and structural elements
- Real-time annotation via similarity search against database
- Translate selections on the fly, or show translation for annotations or selected frame
- Dynamic graphs and statistics for sequence properties such as pI, molecular weight, melting point, AA composition and more
Sequence Alignment
- Multiple and pairwise sequence alignment of DNA or protein including full genome alignment
- Align with trusted algorithms including Geneious Aligner, MUSCLE, MAFFT, Clustal Omega, MAUVE and LastZ
- View and edit alignments with real-time translation and highlighting
Phylogenetics
- Build trees with Geneious tree builder, MrBayes, PAUP*, PhyML, RAxML and more
- Visualize, edit and markup your trees
- Interactive distance matrix viewer
- Publication quality export
Microsatellite Analysis
- Import raw ABI trace files
- Trim, predict and manually adjust peaks
- Bin peaks into alleles
- Produce tabular output of allele calls
Molecular Cloning
- View plasmid maps, automatically annotate vectors, and copy-paste sequences with annotations
- One-step GoldenGate (Type IIS) and Restriction cloning
- Homology-based cloning including Gibson, GeneArt, and In-Fusion
- TOPO cloning
- Parent/descendant lineage tracking of cloning operations
- Codon optimization and back translation
- Silent mutation analysis to find potential restriction sites to introduce
- CRISPR gDNA design
- Simulated PCR, digestion and ligation
Primer Design
- Automatically design PCR and sequencing primers and hybridization probes, to any target region or entire sequence
- Easily add primers in the Sequence View
- Design basic and degenerate PCR primers
- Add and remove extensions to a primer sequence before, during or after the design process
- Primer specificity testing to check for additional binding sites on the template sequence
- Screen for physical properties, hairpins and primer-dimers
- Drag and drop your primers in FASTA, spreadsheet or GenBank format
Data Management and Collaboration
- Drag and drop import of files and folders, including Vector NTI databases
- Import metadata from a spreadsheet onto sequences and other documents
- Smart NGS import – one step import of any assortment of SAM, BAM, GFF, BED, and VCF files
- Intuitive folder-based project organization
- Seamlessly integrated shared database
- Rapid search against all sequences and metadata in your database
- Extensive export options
Searching and BLAST
- Direct access to NCBI public BLAST databases
- Custom BLAST for private local databases
- Integrated search of external databases including GenBank and UniProt
- Upload your sequences directly to GenBank
- Search for literature in PubMed
- Advanced searching against your local or shared database
Automated Workflows
- Create workflows for automated bulk analysis using a visual editor
- More than 20 in-built workflows for performing pipelines including Apply Variants to Reference Sequence, Map Reads then find SNPs, and Randomly Sample Sequences
- Extend capabilities with option to write custom code workflows
API & Developers
- Add specialized functionality or integrate with other systems using the Plugin Development Kit
- Add your favorite algorithm, database or visualization
- Wrap a command line program to run via the Geneious Prime GUI
Geneious Biologics 產品特色
Annotate and Analyze
- Efficiently analyze Sanger and NGS datasets
- Annotate CDR/FR Regions from germline or custom databases
- Highlight sequence features, assets, and liabilities
- Annotate various antibody types including mAb, Fab, scFv, VHH, TCR, and VH/ VL pairs
Identify Statistical Trends
- Cluster sequences by regions or clonotype
- Identify dominant clones
- Group functionally similar sequences
- Compare frequencies across samples
Visualize and Discover
- Integrate assay data
- Search and filter using powerful queries
- View interactive graphs, trees, and alignments
- Build reports with tables, graphs and comments
Manage Data
- Collaborate with team members and share results
- Search for sequences in a central database
- Import and export data seamlessly
- Access a secure and reliable cloud computing platform
Highly Configurable
- Connect important in-house tools, including LIMS, to Geneious Biologics
- Directly share files with Geneious Prime
