Sentence examples for alignment with quality from inspiring English sources

Illumina GA reads were aligned to the bovine and human genome sequences using the software package MAQ (Mapping Alignment with Quality, available from http://maq.sourceforge.net).net

Detailed phylogenomic analysis was performed using a pipeline of hierarchical inference of putative homologs, multiple sequence alignment with quality checking, and phylogenetic inference with trimming to isolate putative sets of orthologs.

On-the-fly alignment was used with quality control samples manually selected as the peak list for primary alignment.

Each alignment was check manually in MEGA 5 [ 21], alignments with poor quality or aligned region <100 bp were discarded.

Alignments with mapping quality <30 (mapQ < 30) were skipped to down-weight the contribution of the low mapping quality reads.

Sequences and alignments with low quality were filtered using Picard68 tools (ver. 2.7.1) and GATK66 software (ver. 3.6 and 3.7), and 734,443 SNP markers in the strains were identified.

Only alignments with mapping quality > 16 were kept.

Only alignments with a quality score ≥ 30 were retained.

Only alignments with mapping quality > = 2 were used for SNP calling.

Duplicates were removed and only alignments with mapping quality greater or equal than 30 were used for further analysis.

Since highly repetitive/low complexity genomic regions may result in ambiguous or low confidence alignments, we conservatively filtered out all alignments with mapping quality (MAPQ) < 35.