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Duplicates removal tool for paired-end

Hi, I used fastuniq, a duplicates removal tool for paired short DNA sequences. It used a lot of memory and I just wonder whether there is another tool which could remove duplication from paired-end with less memory?

Thank you in advance.

Mic

fastq sequence ngs
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updated by i.sudbery i.sudbery • written by Ric Ric

2 answers

You could try the tally tool with reaper. I've only ever use it in single-end mode, but it claims to do paired end as well. As a bonus, it records how many copies of each sequence their were in the read name.

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written by i.sudbery i.sudbery

you could use PRINSEQ or after alignment using samtools also duplicates can be removed. You can go through the links

PCR_duplicates, samtools for duplication

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written by Prasad Prasad

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