GFA 1 graph segments to IMGT (EMBL variant) converter

Convert a GFA 1 graph segments sequence file to IMGT (EMBL variant).

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What kind of sequence is in your file?

This output needs a sequence type. The selected input format does not record it, so the converter will use your choice.

Choose your sequence file

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

GFA 1 graph segments → IMGT (EMBL variant)

Only graph segment sequences are written. Graph links and topology are not preserved.
The output writes every sequence letter in the same case, so lowercase (soft-masked) regions are no longer marked.

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 output needs a sequence type, so replace the example molecule type with DNA, RNA, or protein to match your file.

from Bio import SeqIO

count = SeqIO.convert("input.gfa1", "gfa1",
                      "output.imgt", "imgt",
                      molecule_type="DNA")
print("Converted %i records" % count)

Sample input file: GFA 1 graph segments

Copy this example into a file, or download it, to try a GFA 1 graph segments conversion.

H	VN:Z:1.0
S	segment1	ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG	LN:i:39
S	segment2	TTCGCGATTGTAATGGGCCGCTGA	LN:i:24
S	segment3	GGGTGCCCGATAGCCATTGTAATG	LN:i:24
L	segment1	+	segment2	+	0M
L	segment2	+	segment3	+	0M

Download sample (sample.gfa, 212 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.

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