The Phred quality score can measure the sequence quality, and quality scores are normally stored together with the nucleotide sequence in the widely accepted FASTQ format. For sequence raw reads with various FASTQ formats, the range of scores will depend on the technology and the base caller used. With the different technology, the range of scores is different. For learning the comparing and converting method of sequence Phred quality score, we do an experiment, and analyze the different between various FASTQ quality formats.

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Abstract. The main information of the sequence reads are quality statistics and nucleotide distribution. There are many bioinformatics analysis method to compute quality statistics and create the quality scores and the nucleotide distribution. For learning the sequence reads information of bioinformatics analysis method, we do a sequence reads analysis experiment, and compute quality statistics and create the quality scores and nucleotide distribution graph with the corresponding bioinformatics analysis tools.

Abstract. The initial sequence reads with next-generation sequencing technology have some barcodes or noise, and need to be removed by trimming method of bioinformatics. The trimming method includes trimmer by column with absolute for fixed length reads or percentage for variable length reads and quality trimmer by sliding window. For learning the trimming method of sequence for removing the barcodes or Noise, we do some trimming sequence reads experiments, study the trimmer by column with absolute for fixed length reads or percentage for variable length reads, and compare the results for the different setting of quality score values for the quality trimmer by sliding window.

There are some base characters with specified quality score value in the initial sequence reads. The base characters need the bioinformatics analysis method to mask such as mask by quality score. In the other hand, there are many sequence reads need the bioinformatics analysis method to reverse complement such as reverse-complement. For learning the masking and reverse complement method of the sequence reads, we select some initial sequence reads for the masking and reverse complement experiments, and compare the experiment results of mask by quality score and reverse-complement.