Difference between revisions of "CLCbio Genomics Workbench"

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{{Bioinformatics application
 
{{Bioinformatics application
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|sw summary=De novo and reference assembly of Sanger, 454, Solexa, Helicos, and SOLiD data. Support for paired and single reads. Alignment in base- and color-space, and mixed mode of any of the above including both short and long reads.  Includes tools for SNP and small indel detection and annotation. Runs equally well on Windows, Mac OS X and Linux platforms, plus server/enterprise options for scalability of computation and storage.
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|sw summary=De novo and reference assembly SNP and small indel detection and annotation.
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|bio domain=Genomics, Whole Genome Resequencing, De-novo assembly, SNP discovery, InDel discovery, ChIP-Seq, RNA-Seq and much more...
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|bio domain=Genomics, Whole genome resequencing, Sequence assembly (de novo assembly), SNP detection, Indel detection, ChIP-seq, RNA-Seq, Regulatory RNA, Transcriptomics, Mapping
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|bio method=Mapping, Assembly, and Alignments accelerated with SIMD implementation and multi-threading.
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|bio method=Read mapping, Sequence assembly, Sequence alignment, Ab-initio gene prediction, Adapter removal, Annotation,  Bisulfite mapping, SNP calling,  Sequence assembly (de-novo assembly), Heat map generation, Sequence assembly validation
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Package includes many more common-place bioinformatics tools such as BLAST and Clustal alignments as well.
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|bio tech=454, Illumina, ABI SOLiD, Helicos, Sanger, Ion Torrent,
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|bio tech=454, Illumina, ABI Solid, Helicos, Sanger,
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|created by=Knudsen T, Knudsen B
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|created by=Thomas Knudsen and Bjarne Knudsen et al
 
 
|created at=http://www.clcbio.com
 
|created at=http://www.clcbio.com
 
|maintained=Yes
 
|maintained=Yes
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|input format=FASTA, FASTQ, A reference genome sequence in fasta format, GenBank, SAM, Illumina Bustard, ELAND, CSFASTA/CSQUAL (ABI SOLiD), and many more.
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|input format=FASTA, FASTQ, GenBank, SAM, BAM, Illumina Bustard, ELAND, CSFASTA/CSQUAL (ABI SOLiD)
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|output format=FASTA, FASTQ, GFF, GenBank, SAM, ACE, Nexus, and more
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|output format=FASTA, FASTQ, GFF, GenBank, SAM, BAM,  ACE, Nexus, CSV, PDF, XLS,
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|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.
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|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++
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|licence=Perpetual, temporal, floating network and terminal server licenses available.  Free, limited time trial and evaluation licenses.
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|library=OPEN CLC API for plug in development
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|os=Windows, Mac OS X, Linux, 64 bit
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|licence=Commercial,
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|os=Windows, Mac OS X, Linux
 
}}
 
}}
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Link: http://www.clcbio.com/index.php?id=1240 Category: Integrated solutions
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Server/enterprise options for scalability of computation and storage.
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Package includes many more common-place bioinformatics tools such as BLAST and Clustal alignments as well.
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{{Links}}
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{{References}}
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{{Link box}}

Latest revision as of 10:16, 11 January 2016

Application data

Created by Knudsen T, Knudsen B
Biological application domain(s) Genomics, Whole genome resequencing, Sequence assembly (de novo assembly), SNP detection, Indel detection, ChIP-seq, RNA-Seq, Regulatory RNA, Transcriptomics, Mapping
Principal bioinformatics method(s) Read mapping, Sequence assembly, Sequence alignment, Ab-initio gene prediction, Adapter removal, Annotation, Bisulfite mapping, SNP calling, Sequence assembly (de-novo assembly), Heat map generation, Sequence assembly validation
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.

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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

  1. . 2009. PNAS
  2. . 2009. J. Virol.
  3. . 2009. Mol Plant Microbe Interact.
  4. . 2010. PNAS
  5. . 2010. Nucleic Acids Research
  6. . 2010. Cell Metabolism


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