Sentence examples for based on base quality from inspiring English sources

Reads were trimmed based on base quality (an average phred score of 15 for every four bases) and the presence of adaptor sequences.

Generally, these steps include visualization of base quality scores and nucleotide distributions, trimming of reads and read filtering based on base quality score and sequence properties such as primer contaminations, N content and GC bias.

Reads were mapped against the targeted contigs and then assembled within each cluster using MIRA software [ 91] and SNP detection was performed using stringent criteria based on base quality, absence of heterozygosity within genotypes and 2X minimal allele coverage.

We developed two subset selection methods for single-end reads and a method for paired-end reads based on base quality scores and other read analytic tools using the MapReduce framework.

After filtering out the low quality reads based on base quality value and removing adaptor sequences, 16,834,090 (98.42%) and 19,069,600 (98.49%) clean reads were retrieved, corresponding to 1,058,335 and 977,308 unique sequences, which were the associated counts of the identical sequence reads, respectively.

We also analyzed the mapping efficacy using CLC genomics workbench, of which algorithm is based Smith and Waterman [ 46], after trimming based on base quality (quality score limit = 0.05, removing reads if there are more than 2 ambiguous nucleotides in the reads or less than 15 bp in length).

On the other hand, Novoalign first finds candidate alignment positions from the reference genome for each read, and calculates alignment scores for these positions using the Needleman-Wunsch algorithm, based on base qualities, the existence of gap, and ambiguous codes (Ns).

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

Specifically, for each sample, we (i) trimmed reads to a length of 99 bases, (ii) excluded reads shorter than 99 bases, and (iii) excluded reads with expected error (a measure of read quality in USEARCH based on base call quality and read length) > 0.5.

Remaining reads were trimmed to remove low-quality bases; removing 5 bases from the 5′ end, 7 bases from the 3′ end, and again trimming the 3′ end based on base call quality scores.

This includes the deduplication of clonal reads, filtering based on base call quality, identification of potential bisulfite conversion errors and most notably the detection of single nucleotide variants (SNVs) that would affect methylation calls, the latter of which is until now only being performed by Bis-SNP.