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CLC Assembly Cell
CLC Assembly Cell is a high-performance computing solution for read mapping and de novo assembling of Next Generation Sequencing data.
The command-line interface of CLC Assembly Cell enables the functionalities to be easily included in scripts and other Next Generation Sequencing work-flows.
CLC Assembly Cell is utilizing SIMD instructions to parallelize and accelerate the assembly algorithms, making the program the fastest Next Generation Sequencing assembler at present.
Click here to download a white-paper describing the up to 10-20 times higher speed of CLC Assembly Cell compared to Maq and SOAP when doing Human whole genome read mapping.
Video interviews with customers on de novo assembly – see for yourself!
Click to enlargen.The main functionalities of CLC Assembly Cell are:
- Read mapping
- Read mapping of Illumina Genome Analyzer, SOLiD, and 454 sequencing data
- Support for native Color Space assembly
- Support for both short read and long read assembly, including 454/Titanium data
- Support for both gapped and ungapped alignments when doing short read assemblies
- Support for assembly of paired end reads
- De novo assembly
- De novo assembly of Illumina Genome Analyzer and 454 sequencing data
- Support for both short read and long read assembly, including 454/Titanium
- Support for de novo assembly of paired end data
- Other analyses
- Fast analysis of raw data, including reporting
- Option of joining data from different sources into the same analysis (including data generated by different kinds of sequencing technologies)
- Extraction of data from part(s) of an assembly. Examples are extraction of contig and reads from an area of interest, or extraction (exclusion) of data from a specific sequencing lane that is suspected not to be of acceptable quality.
- Find variations (simple SNP detection)
- Support for input file formats Fasta, Sff, GenBank, csfasta, and scarf
- A number of output options, including tables with assembly info
- A "graphical" (ASCII art :-)) assembly viewer to get quick overview
- Full integration with CLC Genomics Workbench. Output data from CLC Assembly Cell can be imported and further analyzed in CLC Genomics Workbench.
Figure 1: Using SIMD accelerated algorithms, the CLC Assembly Cell performs the assembly very fast. The speed of assembling a data set of 86 million 35 bp reads against the entire human genome (equals about 1 x coverage) is shown below. We have compared with the speed of two of the most popular assembly algorithms for short reads.
CLC Assembly Cells can of course be run in parallel on a multi-node computer cluster. Click here to read more.
CLC Assembly Cell runs on Mac OS X, Windows, and Linux platforms.
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