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. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection, browser and other features. Runs on Windows, Mac OS X and Linux.
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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, InDel discovery, RNA-Seq,
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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, Alignments, command line tool wrappers, genetic variation annotation, Statistics, Visualisation,
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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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|bio tech=454, Illumina, ABI Solid, Helicos, Sanger,
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|bio tech=454, Illumina, ABI SOLiD, Helicos, Sanger, Ion Torrent,
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|created by=Thomas Knudsen and Bjarne Knudsen et al
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|created by=Knudsen T, Knudsen B
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|created at=CLC bio
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|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, 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
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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,  Free trial license
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|library=OPEN CLC API for plug in development
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|os=Windows, Mac OS X, Linux,
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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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