FastQ {SMRUCC.genomics.SequenceModel.FQ}

.NET clr documentation

FastQ

Description

FASTQ 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 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.

There is no standard file extension for a FASTQ file, but .fq and .fastq, are commonly used. (http://en.wikipedia.org/wiki/FASTQ_format)

A FASTQ file normally uses four lines per sequence.

• Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line).
• Line 2 is the raw sequence letters.
• Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.
• Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.

• header
• seuqnece
• +
• quality

一条FastQ序列文件通常使用4行代表一条序列数据：

• 第一行： 起始于@字符，后面跟随着序列的标识符，以及一段可选的摘要描述信息
• 第二行： 原始的序列
• 第三行： 起始于+符号，与第一行的作用类似
• 第四行： 编码了第二行的序列数据的质量高低，长度与第二行相同

Declare

            
# namespace SMRUCC.genomics.SequenceModel.FQ
export class FastQ extends ISequenceModel {
   Headers: string;
   IsProtSource: boolean;
   Length: integer;
   # FastQ.GetQualityOrder() for each char in this string.
   Quality: string;
   # 第一行的摘要描述信息
   SEQ_ID: string;
   # the sequence description information text, but usually be string +.
   SEQ_Info: string;
   SequenceData: string;
}

        

.NET clr type reference tree

1. this class extends from ISequenceModel class: ISequenceModel

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