Multiplexed Pair-End Sequences -- Barcode Sorting

Question

[Johnmu]

Does there exist any tool to do barcode splitting of pair-end sequences?

I realise that FastX toolkit has a barcode splitter. However, it does not work with pair-end sequences since we would need to delete or keep both sequences in the pair.

Anyone know an free software that does this? If not I have have to code one up :(

[Michael]

Isn't fastx_splitter a perl-program? I think we should just add some code to it to allow for paired-end

[Shicheng Guo]

Hi John, What's the possible cost for Multiplexing sequencing for 4096 samples? I am interested to one genomic region (350bp) in 4096 samples? I want to know the cost of this sequencing. Thanks.

[Michael]

You are posting to a very old thread, it is unlikely the original poster will read this.

[Michael]

In addition, I think it is best to simply ask a sequencing provider of your choice for a quote.

Answer 1

[Yannick Wurm]

For a similar issue, Keith suggested the following approach:

1. join paired reads into single megareads (using Galaxy toolkit)
2. do your thing (filtering or barcode splitting)
3. split the concatenated megareads back into paired reads

cheers,
y.

Answer 2

[brentp]

I had the same problem with filtering paired-end reads. In the end, I just wrote a script to call the fastx-toolkit filter on both files and then further filter out reads that were removed from only one of the pairs. Since you know the files come out in the same order, you can do the filtering yourself without reading everything into memory.

So, yes, a custom script is likely your best bet as most existing tools only do a single-end at a time.

[Johnmu]

Thanks for the answer, I'll see what I can do.

Answer 3

[Brad Chapman]

NovoBarCode handles paired end Illumina reads and works with a number of different barcoding schemes:

http://www.novocraft.com/userfiles/file/NovoBarcode.pdf

It's not open source, but is free for academic and non-profit use.