CLCbio Genomics Workbench

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

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