Sentence examples for base calling with a from inspiring English sources

Software Phred [ 60, 61] was used for sequence base calling, with a quality score of Q20.

First, raw sequence data were cleaned up with QCleaner software (Amelieff): low-quality reads (>20% of the base calls with a Phred score <20) were discarded; reads shorter than 32 and reads containing five or more N were also discarded; base calls at both ends with a Phred score <20 were trimmed.

We also filtered out base calls with a quality value below 17, i.e. base calls with an error probability >0.02.

We performed image analysis and base calling with Illumina's RTA v1.13 software and demulitplexed with Illumina's CASAVA v1.8.2.

Base calling with GS-FLX System software generated 353,344 high-quality reads for the first half-run and in 785,322 reads for the second complete run.

Consensus sequences were considered as valid when at least 98% of the nts were base-called with a PHRAP score above 40.

Sequences not meeting our production quality criteria (at least 100 bases called with a quality over 20) were discarded.

After alignment, sequence variants were called based on quantitative thresholds; bases called with a non wild-type frequenon wild-typere attributed to noise, 30% to 70% are called heterozygous changes, and 90% to 100% are called homozygous changes.

Chromatograms were transferred to a Unix workstation, base called with PHRED (v.0.961028), assembled with PHRAP (v. 0.960731), scanned by POLYPHRED (v. 0.970312), and viewed with the CONSED program (v. 4.0).

Sequence reads were base called with Roche base caller version 2.5p1, and the sff files were converted to FASTQ files.

For variant calling using CRISP, reads with low mapping quality (<20) and base calls with a low quality score (<10) were discarded.