Are There Any Tools To Demultiplex An Sff (Or Fastq) File Which Has A Forward And Reverse Barcode?

Question

[Joseph Hughes]

Hi,

I have an sff file of 454 reads that has been tagged with forward and reverse barcodes. The forward barcode is 2bp or 4bp and the reverse barcode is 6bp. Each combination of forward and reverse barcode corresponds to a unique sample which need to be split accordingly. I have been looking for tools that do this, but have only found programs that deal with one barcode per sequence like split_libraries.py and FASTX Barcode Splitter‎. Any suggestions?

Cheers, Joseph

Answer 1

[Istvan Albert]

The computationally challenging part of any barcode splitting process is the approximate matching to allow barcodes with one or more errors in them. Since in your case some of your barcodes are so short the matching approximately won't be of much use. I would recommend writing a tool that does what you need simply matching regular expressions (write a regular expression for each of your barcode pairs).

If you really want to allow approximate matching on the longer barcodes you could split first by the long barcode with fastx toolkit then sub select based on the short barcodes.

If you don't know how to write such a script just post a new question with a short example input and I am sure you'll get some answers.

[Joseph Hughes]

Thanks, I have modified fastx_barcode_splitter to match forward and reverse barcodes allowing for mismatches on the reverse barcode. Cheers, Joseph

[GouthamAtla]

can we use --bol and --eol together ?