Sentence examples for alignment quality filtering from inspiring English sources
However, inference of substitution histories is more difficult in comparison species, whose genome assemblies tend to be lower quality and often lack the resources for proper alignment quality filtering.
Our sequence and alignment quality filters help correct for these differences.
The alignment quality filter discarded 541,122 reads, leaving a total amount of 5,494,405 redundant ISs (the R set).
Finally, we applied an alignment quality filter to the reads in U, discarding all alignments with a BLAST identity score lower than 95% and hs less than 80%.
In addition, since SOAP2 and Bowtie do not have alignment quality scores in their respective output files, to ensure a relatively fair comparison, no alignment quality filters are used.
This is in fact what we can observe in the results shown in Table 4. Improvements on GLAM2's speed and alignment quality after filtering the CFTR dataset with TUIUIU*.
Alignments of the 454 sequencing reads of A. fragilis against the GLEAN3 protein-coding regions of S. purpuratus produced whole-gene alignments for 14,543 genes after quality filtering.
To reduce the number of false-positive indels due to alignment or sequencing errors we applied rigid quality filtering on indels and their flanking regions (see methods).
We aligned the quality filtered sequencing reads with BWA MEM and Bowtie 2, filtered the alignments to the whole exome, and performed base quality score recalibration and indel realignment according to the GATK Best Practices.
(A decent approximation given true-positive rates of >99% in our quality filtered alignments, see Counting False Alignments below).
