2016 tool - native SOLiD (.csfasta and _QV.qual) to colorspace-encoded FastQ
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5.2 years ago
Michael G ▴ 50

The C++ coded tool solid2fastq in the package BFAST was able to merge native SOLiD files (i.e., file.csfasta and file_QV.qual) into a colorspace-encoded FastQ format. Specifically, the sequences remained in colorspace, but the quality values were re-formatted to abide to FastQ specifications.

However, BFAST has not been maintained for years (see GitHub record), and compiling it fails at multiple points, including at the compilation of the above-mentioned tool solid2fastq.

Hence, does someone know an alternative tool or script to conduct the above-mentioned merger? The process is a simple string operation, and there are probably several similar Python- or Perl-scripts saved out there in GitHub space that do it.

P.S. Post Transforming And Manipulating Color Space Reads does a wonderful job in explaining the different colorspace-related conversion processes and has become the main go-to reference on this topic.

conversion SOLiD fastq • 1.5k views
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5.2 years ago
Michael G ▴ 50

Turns out that the Python package ngsutils can do said transformation.

python2 /path_to_github/ngsutils/ngsutils/fastq/fromfasta.py file.csfasta file_QV.qual > file.fastq
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