Convert ABI / AB1 trace (quality trimmed) to QUAL quality scores

Provided by bugaco.com

Convert a ABI / AB1 trace (quality trimmed) sequence file to QUAL quality scores.

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

ABI / AB1 trace (quality trimmed) → QUAL quality scores

  • The called sequence is extracted from the trace; chromatogram data and peak information are not included.
  • QUAL files store quality scores only. Sequence letters are not written.
  • 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.abi-trim", "abi-trim",
                      "output.qual", "qual")
print("Converted %i records" % count)

Sample input file: ABI / AB1 trace (quality trimmed)

ABI / AB1 trace (quality trimmed) is a binary format, so it cannot be shown as text. Download the sample file to try the converter.

Download sample (sample.ab1, 204.3 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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