paired end quality filtering

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

paired end illumina fastq filter

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updated 3.9 years ago by Ram

• written 11.0 years ago by sun.nation

Here is a great solution from Heng Li: Combining The Paired Reads From Illumina Run

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updated 3.9 years ago by Ram

• written 11.0 years ago by Ashutosh Pandey

2 answers

I recommend sickle.

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written 11.0 years ago by Dan D

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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written 11.0 years ago by h.mon

yes quality trimming

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written 11.0 years ago by sun.nation

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