paired end quality filtering
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7.3 years ago
sun.nation ▴ 130

I know it has been asked earlier but not able to find clear solution. I need to filter paired fastq files and align using bowtie2. Is there any tools that I am missing to filter fastq files and keep only paired-end in two different files. And, remaining single reads in another file?

Thanks

SS

paired end illumina fastq filter • 4.2k views
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Here is a great solution from Heng Li: Combining The Paired Reads From Illumina Run

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7.3 years ago
Dan D 7.3k

I recommend sickle.

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7.3 years ago
h.mon 34k

What do you mean by "filter"? Quality trimming? Adapter removal? Contaminant filtering? All of them?

BBDuk and SeqyClean will do all, and will keep proper pairs and a file with singles.

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yes quality trimming

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