How to generate a consensus fasta sequence from SAM tools pileup?
I was trying to convert a fastq consensus sequnece (generated by the mpileup samtools) to a fasta file. However the original FASTQ lines are wrapped. Most of fastq parsers do not work with multi-line fastq files. They only work for 4 lines standard fastq format. Is there a perl script or C# or Java tools to deal with this issue? Please don't use Python, I am not strong on it and I don't want to be an expert on many programming languages during a short time. Of cource, if python is realy powerful, it is considerable.:)
Also if we can get the corresponding quality score for each of the entries, it will be great.