Alignment quality control for minimum percent identity and bi-directional coverage is then performed to remove sequences not meeting these criteria (these values are user-specifiable parameters of the algorithm).
The mpileup command, with –B parameter to disable base alignment quality (BAQ) computation, and the default parameters were used, with the minimum read depth at 10 and the minimum base quality at 30.
¥ Lowest common ancestor (LCA) using 1e-5 cutoff, 60% minimum identity, and a minimum alignment lenght cutoff of 15.
The observations by scanning electron microscope (SEM) suggest ultrahigh alignment density and good alignment quality of SWCNTs.
The alignments were examined and manually trimmed to ensure alignment quality.
Besides alignment quality the sequence composition of the multiple sequence alignment could potentially affect results.
This search identified 708 hits (Eminimum alignment length >50 bp).
Minimum alignment length coverage (-L parameter) varied between 0.1 and 0.9 with step size 0.1.
Quality, read alignment quality.
Structural alignment quality (Z).
