[Biopython-dev] Sequential SFF IO

[Brad Chapman]

Peter;

> Do you have (or can you point me at) any good sample data with
> barcodes, or custom adapters or primer sequences? e.g. some SRA
> numbers you've been using.

This is a subset of two lanes from a barcoded flowcell for testing
purposes:

http://chapmanb.s3.amazonaws.com/110106_FC70BUKAAXX.tar.gz

It has 12 barcoded samples, using the Illumina barcodes. The
sequences are in this YAML file:

https://github.com/chapmanb/bcbb/blob/master/nextgen/tests/data/automated/run_info.yaml

> I originally had three separate tools (with shared code) for working
> with FASTA, FASTQ and SFF reads, which I have recently combined
> into one single tool that does all three. Code here if anyone wants to
> look at it.
> 
> https://bitbucket.org/peterjc/galaxy-central/src/filter_fasta/tools/primers/

Very nice. It would be great to get something general for barcode
splitting as a Galaxy tool. Thanks for looking at this,
Brad