Convert SFF flowgram reads (trimmed) to FASTQ (Sanger PHRED+33)

Provided by bugaco.com

Convert a SFF flowgram reads (trimmed) sequence file to FASTQ (Sanger PHRED+33).

Maximum file size: 50 MB. The file is checked before conversion.

SFF flowgram reads (trimmed) → FASTQ (Sanger PHRED+33)

  • Flowgram signals and other SFF-specific data are not carried over.
  • Quality scores above the output's maximum (93 for Sanger FASTQ, 62 for Illumina and Solexa FASTQ) are capped at that maximum.
  • This input format applies quality trimming and may remove sequence letters.

About this conversion

The converter reads records in the input format and writes them in the output format. Data that the output format cannot store may be lost. The notes under the Convert file button list the important limits for this pair.

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.sff-trim", "sff-trim",
                      "output.fastq", "fastq")
print("Converted %i records" % count)

Sample input file: SFF flowgram reads (trimmed)

SFF flowgram reads (trimmed) is a binary format, so it cannot be shown as text. Download the sample file to try the converter.

Download sample (sample.sff, 17.2 KB)

Samples are small illustrative files. Some come from the Biopython test suite (see the project's sample notes); they are not real study data.

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