It remains to be seen whether this new assembler will work its way into common use in assembly systems such as Phusion and Atlas, but it is unlikely to remain at an advantage for long as the development and advancements of new and reworked as assemblers is swift and continuous.
Well after the completion of this study, a new assembler, VTBuilder [ 124], was published, specifically designed to remedy the deficiencies of Trinity, which typically produces large numbers of incomplete transcripts with highly diversified protein families.
To accomplish this, we used a new assembler, MaSuRCA [ 9], to assemble contigs and scaffolds from this combination of sequences.
Also our new assembler, called IVA (Iterative Virus Assembler), is a completely de novo assembler, whereas PRICE must be provided with seed sequences to be extended into contigs.
In addition, as shown in this study, new assemblers for longer reads are much-needed, since the majority ones were designed for very short reads.
A new assembler-like programming language is also presented, but since the controller is a SoftPLC it is possible to implement even very complicated control algorithms and functions.
A number of new assemblers have been developed for carrying out both de novo and mapped assemblies from new technology reads (Chaisson et al. 2004; Miller et al. 2008).
These problems may be overcome by hybrid sequencing strategies using a mixture of sequencing methodologies, by new assemblers, and by sequencing more deeply.
New assemblers including Velvet (Zerbino and Birney, 2008) offer functionality specifically for short-read sequencing technologies, such as Solexa (Bentley, 2006).
Though PAVE assembles the 454 ESTs with acceptable results, the new short read assemblers that are based on prefix trees and extensions (e.g. SSAKE [ 15]) or de Buijin graphs (e.g. Velvet [ 10], EULER-USR [ 9]) could provide better results when there is a lot of error or repeats.
