Duplicates removal tool for paired-end

Question

[Ric]

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

[Medhat]

Duplicate read removal software tools | NGS - OMICtools

and I suggest MarkDuplicates from picard tools

if desired, duplicates can be removed using the REMOVE_DUPLICATE and REMOVE_SEQUENCING_DUPLICATES options.

[GenoMax]

Since the omics tool does not have dedupe.sh from BBMap: dedupe.sh output from BBTools

Answer 1

[i.sudbery]

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.

Answer 2

[Prasad]

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