Fasta to Fastq Sequence Converter

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Alphabet: None DNA RNA Protein Nucleotide

Input format: fasta This refers to the input FASTA file format introduced for Bill Pearson's FASTA tool, where each record starts with a '>' line. Resulting sequences have a generic alphabet by default.

Output format: fastq FASTQ files are a bit like FASTA files but also include sequencing qualities. In Biopython, 'fastq' refers to Sanger style FASTQ files which encode PHRED qualities using an ASCII offset of 33. See also the incompatible 'fastq-solexa' and 'fastq-illumina' variants.

How to convert from fasta to fastq ?

You can also convert between these formats by using command line tools.
  • On Windows install WSL, on Mac or Linux start terminal
  • Install BioPython
  • Run following script:
    from Bio import SeqIO
    records = SeqIO.parse("THIS_IS_YOUR_INPUT_FILE.fasta", "fasta")
    count = SeqIO.write(records, "THIS_IS_YOUR_OUTPUT_FILE.fastq", "fastq")
    print("Converted %i records" % count)
  • Or you can use this site as online fasta to fastq converter by selecting your formats & file.

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