If you wish to batch-convert hundreds of AB1 files, and you are comfortable with command line and compiling tools, then you can use TraceTuner, see this thread on seqanswers on how to add .fastq support to it.
Another command-line solution would be to use
seqret from the EMBOSS suite:
seqret -sformat abi -osformat fastq -auto -stdout -sequence input.ab1 > output.fastq"
Otherwise, graphical molecular biology programs usually handle AB1 with ease, and will allow conversion.
I realize this is late, but I found an additional way to do this using Biopython, which you have to install prior to the following:
$python3 $from Bio import SeqIO $record = SeqIO.parse("file.ab1", "abi") $count = SeqIO.write(record, "file.fastq", "fastq")