Sentence examples for base quality and alignment from inspiring English sources

These features consist of read statistics provided by an Illumina sequencer (e.g. base quality) and alignment statistics provided by the aligner (e.g. number of matches, mismatches, deletions, insertions, number of possible mappings and mapping quality score).

The final set of features identified fully represents the local and global sequence variation, alignment depth and quality, local and global base quality and sequence alignment quality.

We devised an algorithm, termed GATA, that first forms an assembly from reads partitioned into subsets by targeting arm sequence and then performs base quality– and coverage-informed genotyping by alignment of raw reads back to the assembled contigs.

However, starting from the output of HTS alignments, filters for base quality, alignment quality and coverage must be applied prior to variant calling.

Smith et al. [50] found that using base quality scores improves alignment accuracy if the aligner uses lower penalties for an error-prone mismatch.

We also tested whether local realignment reads around insertions and deletions and base quality re-calibration (post-alignment processing tools in the GATK package) improved results.

As with Bowtie2, Stampy also considers base quality calls, and allows gaps in this alignment step.

Estimation of nucleotide-read error is based on base-quality and mapping-quality scores from image analysis and alignment.

The sequencing reads were aligned to the reference genome using BWA [ 24], then preprocessed according to Broad best practice guidance (indel realignment, base quality score recalibration, and base alignment quality scoring).

Base calling, quality trimming and alignment of ABI chromatograms was performed using SeqScape v2.5 (Applied Biosystems).

Base calling, quality trimming and alignment of ABI chromatograms was performed using SeqScape Software v2.5 (Applied Biosystems).