Barcode splitter - for paired end reads & specifiy prefix in output file

[spoonman]

Hi,
I'm new to SEQanswers, and more or less new to NGS data (since Juli).
I'm looking for a barcode splitter that
1.) can handle Illumina paired end reads (keeps them as paired end after splitting)
2.) lets you specifiy a prefix for the output files (makes it easier for usage in a pipeline)

I know barcode splitters like Novobarcode that can handle case 1.) or fastx barcode splitter that offers case 2.) Does anyone know a barcode splitter that combines both features?

Thanks in advance for any hint, really appreciate it!

spoonman

[greigite]

I don't know a tool that combines both, but a work-around pipeline might be to:
1) split read 1 file with fastx_barcode_splitter
2) construct lists of reads from each library
3) extract those reads from the original read 2 file using cdbyank or Galaxy tools (seq_filter_by_id.py)

[cswarth]

Originally Posted by greigite

I don't know a tool that combines both, but a work-around pipeline might be to:
1) split read 1 file with fastx_barcode_splitter

In my experience fastx_barcode_splitter cannot be used to split illumina barcode output. Maybe our sequencing guys have a non-standard setup, but when we get illumina barcode results they are split into two files; one with the sequences and another file with just the barcodes. Is this normal?

fastx_barcode_splitter seems to assume that the barcode is at the 3' end of each read, which in our case is not true. We have to match up lines from one file with lines from the other to split the data by barcode.

I ended up writing a perl script (loosely based on fastx_barcode_splitter.pl) that handled the case of barcodes in a separate file from the main sequencing results.