Quality-filtered sequences were aligned using the Silva 16S reference alignment, screened to include only overlapping regions of sequence, pre-clustered (diffs=2), and chimera checked (uchime).
BSA data analysis is non-trivial due to sequencing, alignment and screening errors.
The alignment was screened to remove poorly aligned sequences using vertical = T and trump = options in mothur.
KN and RC participated in the sequence alignment and screened of subjects.
First, our general alignment was screened by eye for the presence of specific sequence signatures, as described above.
The 31 genes selected for a MLST approach and its corresponding concatenated alignment, were screened for the presence of putative recombination events by using RDP 2.0b08 [ 82].
The genome sequences were then aligned to the reference genome sequence and alignments were screened for SNPs.
Alignments were screened for regions with high abundance of non-coding regions.
Both the forward and backward strand of the alignments were screened separately.
All remaining alignments were screened for the presence of phylogenetic signal using the Permutation Tail Probability (PTP) test [ 32, 33].
