Difference between revisions of "CLCbio Genomics Workbench"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=De novo and reference assembly SNP and small indel detection and annotation. | |sw summary=De novo and reference assembly SNP and small indel detection and annotation. | ||
− | |bio domain=Genomics, Whole Genome Resequencing, De-novo assembly, SNP discovery, InDel discovery, ChIP-Seq, RNA-Seq | + | |bio domain=Genomics, Whole Genome Resequencing, De-novo assembly, SNP discovery, InDel discovery, ChIP-Seq, RNA-Seq, RNA-Seq, miRNA, Transcriptomics, |
− | |bio method=Mapping, Assembly, Alignment, Colorspace, BLAST, Ab-inito gene prediction, Adapter Removal | + | |bio method=Mapping, Assembly, Alignment, Colorspace, BLAST, Ab-inito gene prediction, Adapter Removal, Annotation, Assembly QC, Basespace, Bisulfite SNP calling, De Bruijn graph, Heatmaps, |
− | |bio tech=454, Illumina, ABI SOLiD, Helicos, Sanger, Ion Torrent | + | |bio tech=454, Illumina, ABI SOLiD, Helicos, Sanger, Ion Torrent, |
|created by=Knudsen T, Knudsen B | |created by=Knudsen T, Knudsen B | ||
|created at=http://www.clcbio.com | |created at=http://www.clcbio.com | ||
|maintained=Yes | |maintained=Yes | ||
|input format=FASTA, FASTQ, GenBank, SAM, BAM, Illumina Bustard, ELAND, CSFASTA/CSQUAL (ABI SOLiD) | |input format=FASTA, FASTQ, GenBank, SAM, BAM, Illumina Bustard, ELAND, CSFASTA/CSQUAL (ABI SOLiD) | ||
− | |output format=FASTA, FASTQ, GFF, GenBank, SAM, BAM, ACE, Nexus, CSV, PDF, XLS, | + | |output format=FASTA, FASTQ, GFF, GenBank, SAM, BAM, ACE, Nexus, CSV, PDF, XLS, |
|sw feature=Advanced and user-friendly analyses of genomic, transcriptomic, and epigenomic NGS data in a graphical user-interface. Wizard driven tools and a freely available developer toolkit, SIMD implementation, multi-threading, hybrid assembly, Integrated solution, | |sw feature=Advanced and user-friendly analyses of genomic, transcriptomic, and epigenomic NGS data in a graphical user-interface. Wizard driven tools and a freely available developer toolkit, SIMD implementation, multi-threading, hybrid assembly, Integrated solution, | ||
|language=Java, C++ | |language=Java, C++ |
Revision as of 10:03, 1 August 2013
Application data |
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Created by | Knudsen T, Knudsen B |
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Biological application domain(s) | Genomics, Whole Genome Resequencing, De-novo assembly, SNP discovery, InDel discovery, ChIP-Seq, RNA-Seq, RNA-Seq, miRNA, Transcriptomics |
Principal bioinformatics method(s) | Mapping, Assembly, Alignment, Colorspace, BLAST, Ab-inito gene prediction, Adapter Removal, Annotation, Assembly QC, Basespace, Bisulfite SNP calling, De Bruijn graph, Heatmaps |
Technology | 454, Illumina, ABI SOLiD, Helicos, Sanger, Ion Torrent |
Created at | http://www.clcbio.com |
Maintained? | Yes |
Input format(s) | FASTA, FASTQ, GenBank, SAM, BAM, Illumina Bustard, ELAND, CSFASTA/CSQUAL (ABI SOLiD) |
Output format(s) | FASTA, FASTQ, GFF, GenBank, SAM, BAM, ACE, Nexus, CSV, PDF, XLS |
Software features | Advanced and user-friendly analyses of genomic, transcriptomic, and epigenomic NGS data in a graphical user-interface. Wizard driven tools and a freely available developer toolkit, SIMD implementation, multi-threading, hybrid assembly, Integrated solution |
Programming language(s) | Java, C++ |
Software libraries | OPEN CLC API for plug in development |
Licence | Commercial |
Operating system(s) | Windows, Mac OS X, Linux |
Summary: De novo and reference assembly SNP and small indel detection and annotation.
"Error: no local variable "counter" was set." is not a number.
Server/enterprise options for scalability of computation and storage.
Package includes many more common-place bioinformatics tools such as BLAST and Clustal alignments as well.
Links
References
- . 2009. PNAS
- . 2009. J. Virol.
- . 2009. Mol Plant Microbe Interact.
- . 2010. PNAS
- . 2010. Nucleic Acids Research
- . 2010. Cell Metabolism
To add a reference for CLCbio Genomics Workbench, enter the PubMed ID in the field below and click 'Add'.
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