Convert ACE assembly contigs to SeqXML

Provided by bugaco.com

Convert a ACE assembly contigs sequence file to SeqXML.

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

ACE assembly contigs → SeqXML

  • Contig sequences are extracted. Read placement and assembly details are not preserved.
  • This input format always holds DNA, so the output records are labeled as DNA.
  • The output keeps sequence letters but removes per-base quality scores.

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 input format always holds DNA but does not record it, so the molecule type is set explicitly.

from Bio import SeqIO

count = SeqIO.convert("input.ace", "ace",
                      "output.seqxml", "seqxml",
                      molecule_type="DNA")
print("Converted %i records" % count)

Sample input file: ACE assembly contigs

Copy this example into a file, or download it, to try a ACE assembly contigs conversion.

Download sample (sample.ace, 10.5 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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