Question

A preprocessing step performed on reads before they are assembled is quality filtering and quality trimming. In these procedures reads that do not have a mean or median quality score above a certain threshold are removed. Also, portions of reads that do not have a mean or median quality score above a certain threshold are removed; i.e. the reads are "trimmed". The default threshold is often a quality score of 13. Why might this be? Answer the question considering the meaning of quality scores in a FASTQ file.

Answer 1

Answer:

• Although very aggressive quality trimming is common, this study suggests that a more gentleFASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores.
• Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.
• It was originally developed at the Wellcome Trust Sanger Institute to bundle a FASTA formatted sequence and its quality data, but has recently become the de facto standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer.
• trimming, specifically of those nucleotides whose PHRED score <2 or <5, is optimal for most studies across a wide variety of metrics.
• Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.
• The selection of trimming steps and their associated parameters are supplied on the command line.

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