Convert FASTQ (Solexa+64) to NEXUS alignment

Provided by bugaco.com

Convert a FASTQ (Solexa+64) sequence file to NEXUS alignment.

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

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

FASTQ (Solexa+64) → NEXUS alignment

  • The output keeps sequence letters but removes per-base quality scores.
  • The selected output is an alignment format. Every sequence must be the same length and already aligned. This does not create an alignment.
  • The output keeps only each record's ID, so description text (such as the words after the ID on a FASTA header line) is not kept.

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.fastq-solexa", "fastq-solexa",
                      "output.nexus", "nexus",
                      molecule_type="DNA")
print("Converted %i records" % count)

Sample input file: FASTQ (Solexa+64)

Copy this example into a file, or download it, to try a FASTQ (Solexa+64) 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.

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