9.2 years ago by
Roche's "Newbler" gsAssembler and MIRA will both output FASTA+QUAL files for their contigs, which you can turn into a Sanger FASTQ file. They also output ACE files for the contigs which can also be converted into FASTQ files.
For MIRA the contigs have PHRED quality scores as high as 90, while for the Newbler assembly I just looked at the scores went up to 64. These scores are much higher than any single read (typically maximum PHRED 40) because they are based on a consensus.
You can probably do this for other quality aware assembler output too.