Converting Bcl To Fastq

Question

[Pierre Lindenbaum]

Hi all,

I've been asked to convert some Illumina BCL files to FASTQ.

How can I perform this ? Do I really need CASAVA (which is still not installed here) ?

Thank you

Pierre

[Arun]

AFAIK this should be done at the sequencing center? From my search, I was able to find only CASAVA's configureBclToFastq.pl script that performs this conversion.

[Pierre Lindenbaum]

The HiSeq sequencer has been installed but we're waiting for Casava; We'd like to perform some basic tests.

[Arun]

In that case, I am not quite sure about the licensing restrictions. But if you wish to play around, here's a google hit on casava 1.8.2. http://www.umanitoba.ca/afs/Plant_Science/psgendb/local/pkg/CASAVA_v1.8.2/

[Rm]

So far I could not find any alternative: Once you register with Illumina: It will let you download latest casava from https://my.illumina.com/Download/Index

Answer 1

[Pablo Marin-Garcia]

An update on this:

Illumina has released an standalone bcl2fastq program (now at version 1.8.4) that is also capable to take as input gziped bcl files:

http://support.illumina.com/downloads/bcl2fastq_conversion_software_184.ilmn

[Pierre Lindenbaum]

thank you Pablo.

Answer 2

[Istvan Albert]

You probably only need the offline basecaller, this not the entire casava pipeline (that the OBL is part of) this still a sizeable software to install.

http://www.illumina.com/support/sequencing/sequencing_software/offline_basecaller_olb.ilmn

Since this is such a vendor specific format plus it is produced early in the process I don't know of any other tool to do it.

[Pierre Lindenbaum]

thank you, I'll test this tomorrow morning

[Istvan Albert]

forgot to mention that this may only do bcl to qseq transformation, the qseq is a tab delimited format that looks like:

#    qseq format
#    0. machine name: identifier of the sequencer
#    1. run number: number to identify the run on the sequencer
#    2. lane number: positive integer (currently 1-8)
#    3. tile number: positive integer
#    4. X: x coordinate of the spot (integer)
#    5. Y: y coordinate of the spot (integer)
#    6. index: index sequence or 0 (no indexing, or file that has not
#              been demultiplexed)
#    7. read number: 1 - single reads
#                    1 or 2 - paired ends or multiplexed single reads
#                    1, 2, or 3 - multiplexed paired ends
#    8. sequence: called sequence of read
#    9. quality: the quality string
#   10. filter: 0 - read did not pass quality filtering
#               1 - read passed quality filtering

[Pablo Marin-Garcia]

Since casava 1.8.0 you have configureBclToFastq.pl that converts bcl to fastq and demultiplex them if you have used barcodes.

Answer 3

[Jim Vallandingham]

Would it be possible to do this with Picard? Specifically, Picard's IlluminaBasecallsToSam

Picard - IlluminaBasecallsToSam

Then, if needed, using * SamToFastq* also from Picard.

If you have the entire basecalls directory, this might be worth checking out. I don't see a lot of documentation... a potentially relevant SEQAnswers question is unaddressed:

SEQAnswers question on IlluminaBasecallsToSam