paired end quality filtering

Question

[sun.nation]

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

[Ashutosh Pandey]

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

Answer 1

[Dan D]

I recommend sickle.

Answer 2

[h.mon]

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.

[sun.nation]

yes quality trimming