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Bio::SeqIO::fastq 1.4

  Date Added: June 10, 2010  |  Visits: 1.275

Bio::SeqIO::fastq

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Bio::SeqIO::fastq is a fastq sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. This object can transform Bio::Seq and Bio::Seq::SeqWithQuality objects to and from fastq flat file databases. Fastq is a file format used frequently at the Sanger Centre to bundle a fasta sequence and its quality data. A typical fastaq entry takes the from: @HCDPQ1D0501 GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT..... +HCDPQ1D0501 !*((((***+))%%%++)(%%%%).1***-+*))**55CCF>>>>>>CCCCCCC65..... Fastq files have sequence and quality data on a single line and the quality values are single-byte encoded. To retrieve the decimal values for qualities you need to subtract 33 (or Octal 41) from each byte and then convert to a 2 digit + 1 space integer. You can check if 33 is the right number because the first byte which is always ! corresponds to a quality value of 0..

Requirements: No special requirements
Platforms: Linux
Keyword: Bioseqiofastq Fastq Input Output Libraries Programming Quality Seqio Sequence
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License: Freeware Size: 4.7 MB
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