We based the preliminary assessment of assembly quality on the first part of the first stage, and optimized our assembly parameters, using the pre-unitig contiguity statistics (Fig. 1).
As more purpose built de-novo transcript assemblers become available there is a need for a systematic assessment of assembly tools and sequencing protocols for Illumina metatranscriptome data.
The main aspects of the COMPASS RICH-1 photon detectors upgrade are presented focussing on detector design, engineering aspects, mass production, the quality assessment and assembly challenges of the MPGD components.
Additional file 1: Assessment of assembly quality.
Secondly, our assessment of assembly quality found no evidence for selective amplification of unannotated sequences.
These datasets are not independent, but each offers a different assessment of assembly quality.
The computer programs PHRED, PHRAP and CONSED were used to perform base calling and quality assessment, sequence assembly and contigs ordering for each BAC clone (Ewing and Green, 1998; Gordon et al, 1998).
Finally, a stringent assessment of assembly performance was performed by calculating the number of CCDS represented in a TA which had a >=90% CRR.
Base calling, quality assessment, and assembly were carried out using the Phred and Phrap (Ewing et al. 1998) and Consed (Gordon et al. 1998).
Sequence quality assessment and assembly were performed with a quality of less than 1 error in 100,000 bases using PHRAP [ 61] and Consed [ 62].
