The phrase "alignment quality threshold" is correct and usable in written English.
It can be used in contexts related to measurement, evaluation, or standards, particularly in fields like data analysis, machine learning, or quality control.
Example: "We need to establish an alignment quality threshold to ensure that our models meet the required performance standards."
Alternatives: "quality alignment limit" or "alignment performance benchmark".
For queries aligning to more than one place on the genome, strategies vary among the tools, with some reporting all alignments above certain quality threshold and others attempting to rank the alignments and report a fixed number of the top-ranking alignments.
Alignment quality-control thresholds were set as follows: E-value cutoff 1e-150, number of alignments 1, output format 0, number of descriptions 1.
In order to minimize the mining of technical errors we defined a stringent threshold for alignment quality (expect≤1E-21) and the low quality ends of alignments were discarded.
Using AA-ALIGNER, we determined the effect of experimental and analytical variables such as sequence read length, sequencing depth, number of mismatches allowed during alignment, and imputation quality thresholds on accurate allelic imbalance detection.
Furthermore, the output of NextGenMap+MaxSSmap reveals many high scoring alignments well above the mapping quality threshold that warrant further study.
During the alignment, the "-m" setting for mismatches was set at default to allow GSNAP to auto set the number of allowed mismatches based on read length, which allowed for the best alignment across intron-exon boundaries GSNAP "soft-trims" reads during the alignment process, so that only portions of the reads above the quality threshold are aligned.
First, pileups were generated using 'mpileup' command with probabilistic realignment for the computation of base alignment quality (BAQ) disabled and maximum coverage threshold set to 50,000.
Alignment files were further filtered for mapping quality (threshold 75), number of mismatches to the reference ('ΝΜ' threshold 10) and for proper pair mapping with BamTools [ 71].
While these results focus on the accuracy of the MRF score for the remote homolog decision problem, as opposed to the question of alignment quality, we note that SMURFLite with an interleave threshold of 1 or 2 produces highly similar alignments to full SMURF, particularly with respect to placing the 'blades' of the 6-, 7- and 8-bladed propellers.
