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Old 01-20-2011, 08:50 AM   #16
Location: california

Join Date: Jul 2009
Posts: 24


It's great to hear the news, and I'm very concern on the speed for bcl converter in CASAVA1.8. How many hours do we need to get a compressed FASTQ for a typical Hiseq 2000 run (with and without multiplexing)? And how about its parallelization support? Thanks.


Originally Posted by skruglyak View Post
Hi everyone,

my name is Semyon and I work in Bioinformatics at Illumina. Our team has prepared a document describing the major changes planned in CASAVA 1.8. The document is available at iCom and attached to this post. I will do my best to follow the thread and answer any questions that you may have. Early access of the release is planned for late February.

The key changes are:

1. The bcl converter will be distributed with CASAVA.
2. The converter will produce compressed FASTQ files rather than qseq files.
3. The FASTQ quality score encoding will use the standard offset value of 33 rather than the previous Illumina-specific offset value of 64.
4. If samples have been multiplexed in a sequencing run using indexing, the converter will also perform demultiplexing.
5. The output files will be in a directory structure organized by project and sample rather than lane and tile.
6. The GERALD summary file will be modified in accordance with the new directory structure.
7. The sequence output of post-alignment analysis will be a set of BAM files.


Last edited by Auction; 01-20-2011 at 09:00 AM.
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