CLCbio Genomics Workbench

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Application data

Created by Knudsen T, Knudsen B
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.

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. Zhao Q, Caballero OL, Levy S, Stevenson BJ, Iseli C, de Souza SJ, Galante PA, Busam D, Leversha MA, Chadalavada K, Rogers YH, Venter JC, Simpson AJ, Strausberg RL.. 2009. PNAS
  2. Wen KW, Dittmer DP, Damania B.. 2009. J. Virol.
  3. Tyler HL, Roesch LF, Gowda S, Dawson WO, Triplett EW.. 2009. Mol Plant Microbe Interact.
  4. Anthony S. Amend, Keith A. Seifert, Robert Samson, and Thomas D. Bruns. 2010. PNAS
  5. Petrie KL, Joyce GF.. 2010. Nucleic Acids Research
  6. Williams SL, Huang J, Edwards YJ, Ulloa RH, Dillon LM, Prolla TA, Vance JM, Moraes CT, Züchner S.. 2010. Cell Metabolism


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