Specific characteristics of CLC bio's algorithmThere are some advantages and some disadvantages of CLC bio's algorithm when compared to other programs such as Velvet[Zerbino and Birney, 2008] and SOAPdenovo[Li et al., 2010]. The advantages are:
clc_assemblerdoes not use as much RAM as other programs
clc_assemblerprogram is quite fast
clc_assemblerreadily uses data from mixed sequencing platforms (Sanger, 454, Illumina, SOLiD5.1, etc).
The reason that we are able to use little RAM compared to other programs is that we have a very strong focus on keeping the data structures very compact. When appropriate, we also use the hard drive for temporary data rather than using RAM.
The speed of the assembly program has been achieved by threading many parts of the program to use all available CPU cores. Also, some parts of the program are done using assembler code including SIMD vector instructions to get the optimal performance.
- ... SOLiD5.1
- See how SOLiD is supported in SOLiD support in de novo assembly