If the target size is small, then only a small number of contacts between the protein and the DNA can be utilized to read out genomic information and sequence space is consequently minimal.
The nucleotide sequence is determined for each read by the base-caller; the assembler then is utilized to piece the reads together into their original order, but must account for insertions, deletions, rearrangements, inversions, and sequence divergence in doing so.
On each platform, for each base in reads, image parameters such as intensity level, background and noise are utilized to generate reads and quality scores.
The MG-RAST v.3.0 online server quality control pipeline was utilized to remove reads of short length and poor quality before annotation and the analysis of metagenomic data [ 26].
Cross_match (Phil Green, http://www.phrap.org) was utilized to align the reads assigned to each bin to the corresponding ~100 kb of genomic sequence.
Mothur (http://www.mothur.org/) was utilized to analyze the pyrosequencing reads.
Then TopHat was utilized to align these reads to the reference genome permitting four mismatches considering their germplasm variances.
The directionality of the reads was utilized to refine the peak boundaries.
Powerful computer algorithms are then utilized to piece the resulting sequence reads back together into longer continuous stretches of sequence (contigs), a process known as de novo assembly.
