I am looking for a script that can produce an interleaved fastq file and a file of orphaned [single end] reads from two input fastq files. The two read pairs have been quality filtered using fastx-toolkit 'fastq_quality_filter', which breaks the exact pairing that previously existed.
Has anyone come across a script to do this rather than just to interleave two perfectly paired sets of fastq files?
Has anyone come across a script to do this rather than just to interleave two perfectly paired sets of fastq files?
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