I have a large collection of sequence trace files which are in SCF file format (binary files that in addition to the string of DNA bases also contain the electropherogram of the sample and quality information about the base calls).
I have an existing BioPython pipeline that accepts files in AB1 format (pdf), so I need to convert my SCF files to AB1 files.
I found a question on Biostars that asks for the opposite: converting from SCF to AB1.
The accepted answer there was to use
convert_trace from the Staden package.
./convert_trace -out_format scf < trace.ab1 > trace.scf
So I tried the opposite:
./convert_trace -out_format abi < trace.scf > trace.ab1
This did indeed produce a file with
*.ab1 extension, but upon importing it to my BioPython pipeline, I got the error
File should start ABIF, not '\xaeZTR'
convert_trace converted my files to ZTR format, even altough I specified
Closer reading of the manual states that
[convert_exe] can write CTF, EXP, PLN, SCF and ZTR formats. (so indeed no ABI), but it confuses me why
ABI is still a valid output format.
So, my question is, how do I convert SCF files into ABI files?