I got some 16s (forward and reverse) sanger sequencing data (from ABI 3730xl DNA) from our on campus sequencing facility. They came in abi format but the quality scores have not been applied. When I asked for quality scores, the staff at the sequencing facility used KB Basecaller but also warned me that those scores are inflated. The staff recommended Staden, which gives quality score close enough to true Phred score, but it is not command-line based, therefore not good for batch processing. Phred is command-line based but it is not free. It seems like the Phred score calculation is patented (https://www.google.ch/patents/US6681186) and maybe that's why it is hard to find a tool?
Ideally I would like to have the quality score applied to those trace files so I can start the trimming and merging process. I've only worked with next-generation sequencing data and was always given fastq files. Therefore I was also wondering whether it is normal to be provided with trace files without quality score applied.
Any advice is appreciated.