Convert Sanger FASTQ reads to FASTA sequences; quality scores are removed.
Dropping the quality scores to get plain FASTA reads
Yes, this page converts FASTQ (Sanger PHRED+33) to FASTA. The sequence letters are kept and the per-base quality scores are removed, because the output format has no place for them, and no sequence-type question is asked for this pair. In the sample on this page, each of the three reads becomes one FASTA record with its name unchanged.
What carries over from each read
| Data in your file | In the output | Details |
|---|---|---|
| Read letters | Kept | In the sample, three reads of 60, 48, and 50 letters come through unchanged. |
| Read names | Kept in the sample | The sample's first header line reads >read1 example read 1. |
| Text after the read name | Kept in the sample | Unchanged in the sample. |
| Per-base quality scores | Lost | Removed. Keep the original FASTQ file if a later step needs them. |
Other FASTQ encodings
This page reads Sanger PHRED+33. FASTQ (Illumina PHRED+64) to FASTA and FASTQ (Solexa+64) to FASTA read those two encodings and drop the scores in the same way. This route does not check the quality characters, because FASTA output stores no scores. A PHRED+64 file uploaded here as Sanger FASTQ is therefore not flagged; its scores are discarded either way.
Keeping the quality scores
FASTQ (Sanger PHRED+33) to QUAL quality scores writes the scores without sequence letters. If you need both, convert the same file here and on that page; you get the letters and the scores in separate files.
Why FASTA cannot be converted back to FASTQ
The reverse direction, FASTA to FASTQ (Sanger PHRED+33), is blocked: the input has no per-base quality scores, so a FASTQ file cannot be created from it alone. The site suggests starting from a file that has scores, such as FASTQ, PHD, SFF, an ABI trace, or ACE, or choosing a sequence-only output.
If the converter refuses the file
If the upload cannot be read, the page says only that it could not be read as FASTQ (Sanger PHRED+33) and asks you to check that it is a valid file; no cause is given. Uploads are limited to 50 MB.
Run it with Biopython
For batch work, you can use Biopython's SeqIO.convert function. This pair needs no molecule type argument.
from Bio import SeqIO
count = SeqIO.convert("input.fastq", "fastq",
"output.fasta", "fasta")
print("Converted %i records" % count)Sample input file: FASTQ (Sanger PHRED+33)
Copy this example into a file, or download it, to try a FASTQ (Sanger PHRED+33) conversion.
Download sample (sample.fastq, 394 bytes)
Samples are small illustrative files. Some come from the Biopython test suite (see the project's sample notes); they are not real study data.