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FASTA and FASTQ Data Types

This page documents FASTA and FASTQ file handling in Mycelia.

Reading Files

Functions for reading sequence data from FASTA and FASTQ files.

FASTA Readers

  • Standard FASTA parsing
  • Indexed FASTA access
  • Streaming large files

FASTQ Readers

  • Quality score handling
  • Read filtering during parsing
  • Paired-end read management

Writing Files

Functions for writing sequence data to FASTA and FASTQ files.

FASTA Writers

  • Standard FASTA output
  • Formatted sequence output
  • Compressed file support

FASTQ Writers

  • Quality score preservation
  • Format conversion
  • Filtered output