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[fasta|fastq] is an input file of sequence data in fasta/fastq format, and options are additional parameters that can be found in the PRINSEQ manual: prinseq.sourceforge.net/manual.html. The output format (-out_format) can be 1 (fasta only), 2 (fasta and qual), 3 (fastq), 4 (fastq and input fasta), and 5 (fastq, fasta and qual)
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25 Dec 2012 Introduction. PRINSEQ is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. It is particular designed for 454/Roche data, but can also be used for other types of sequence data. PRINSEQ is available through a
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