Sanger to fastq

Created in May 25, 2024

2024   ·   code  

Sometimes we find ourselves with some Sanger data that we would like to use to prototype an NGS workflow. Here’s a script to turn a list of ab1 files into a single fastq file suitable for that.

from Bio import SeqIO

# list of ab1 files
files = ["1.ab1", "2.ab1"]

records = []

for file in files:
    record = next(SeqIO.parse(file, "abi"))

SeqIO.write(records, "all_out.fastq", "fastq")