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format-conversion

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Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL, Stockholm) and re-encode FASTQ quality offsets using Biopython Bio.SeqIO. Use when changing a file format for a downstream tool, fixing FASTQ quality encoding (Phred+33 vs Phred+64 vs Solexa), or when a conversion risks silently dropping annotations or quality scores.

When to use

• changing a file format for a downstream tool
• fixing FASTQ quality encoding
• converting GenBank to FASTA
• re-encoding Phred+64 to Phred+33
• streaming one-shot conversion
• converting Stockholm to FASTA

When not to use

• tasks where conversion risks silently dropping annotations or quality scores without explicit handling

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