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We chose assembly conditions that included a high salt concentration (600 mM NaCl) and an increased temperature (37 °C) to facilitate comparison of the Cp149ox and Cp149red assembly reactions.
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When choosing assembly tools, says Rhie, one consideration is the number of repeat sequences in a genome.
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It is observed that there is a learning process of the chosen assembly method, since the assembly times were reduced with the training sessions.
Using a frequency analysis of hand velocities, errors in the chosen assembly method were revealed showing differences in the hand velocities.
Thus, by the chosen assembly strategy we can estimate that about 1.1 mis-assemblies (9 in 8 BAC assemblies) can be expected per BAC, preferentially in repetitive regions.
When choosing assembly software, it is important to consider both the amount of sequencing data and which computational resources are available (Schatz et al. 2010a).
Considering that we used single reads instead of paired-end reads, this indicates that the chosen assembly strategy (pre-processing of the raw reads followed by multi-k-mer assembly using Velvet and super-assembly using CAP3) was successful.
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CEO of Professional Science Editing for Scientists @ prosciediting.com