Demultiplexing bcl files into fastq files

Question

[Javad]

Hello,

I have bcl formatted files generated by illumina nextseq 500 machine and I want to demultiplex them into fastq files. I can not install the software provided by illumina (bcl2fastq2) on my machine because apparently it is not compatible with ubuntu 16.04. Is there any other tool that can be used for demultiplexing bcl files?

Thanks in advance

[igor]

Have you tried this solution for Ubuntu 14.04?

It sounds like boost 1.54 is the biggest complication.

Answer 1

[Dan D]

Picard has a BCL-to-FASTQ conversion tool that's not quite as robust as Illumina's proprietary tool. It might be worth a shot:

Answer 2

[chen]

I am running bcl2fastq on ubuntu 14.04 and 16.04, both working well.

If you cannot run it, post the error messages here.

Answer 3

[GenoMax]

No that is your only option.

Someone recently installed it on ubuntu. Follow the discussion here: Issues installing bcl2fastq?

If this is a one time request you really should get the facility that produced the sequence to do the demultiplexing for you.

[ATpoint]

Just out of curiosity: Isn't it normal that you get fastq from the facilities. We never had it that they provided the raw calls, unless especially requested.