Stockholm to Fastq-solexa Sequence Converter

Input format: stockholm The Stockholm alignment format is also known as PFAM format.

Output format: fastq-solexa FASTQ files are a bit like FASTA files but also include sequencing qualities. In Biopython, 'fastq' refers to Sanger style FASTQ files which encode PHRED qualities using an ASCII offset of 33. See also the incompatible 'fastq-solexa' and 'fastq-illumina' variants.

You can also convert between these formats by using command line tools.

On Windows install WSL, on Mac or Linux start terminal

Install BioPython

Run following script:

from Bio import SeqIO

records = SeqIO.parse("THIS_IS_YOUR_INPUT_FILE.stockholm", "stockholm")
count = SeqIO.write(records, "THIS_IS_YOUR_OUTPUT_FILE.fastq-solexa", "fastq-solexa")
print("Converted %i records" % count)

Or you can use this site as online stockholm to fastq-solexa converter by selecting your formats & file.