Converting .Bcl To Fasta

Question

[Kash]

Hi all,

I want to know how to convert .bcl files to FASTA format as most of the tools take inputs in FASTA form. Hope some one can help me.

[Neilfws]

What have you tried so far? Google suggests that conversion to FASTQ, rather than FASTA, might be what you want.

[Keith Callenberg]

Similar question here: Converting Bcl To Fastq

I think the best solution right now is bcl2fastq: http://support.illumina.com/downloads/bcl2fastq_conversion_software_184.html. It is a standalone app released by Illumina, although it may not be supported in the future as they put more resources into BaseSpace.

Answer 1

[Ido Tamir]

Neil is correct, you will either get fastq output or sam/bam. For both exist converters and filters (the qualities serve a purpose) to fasta. And most NGS tools actually use fastq not fasta as input.

• https://github.com/wtsi-npg/illumina2bam which is easy to use (I use it in our pipeline)
• http://picard.sourceforge.net/command-line-overview.shtml#IlluminaBasecallsToFastq
• CASAVA from illumina

[Dan D]

The above answer is pretty comprehensive, but if indeed you want to go from FASTQ to FASTA, then the FASTX toolkit--among many other programs--has a module for that:

http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastq_to_fasta_usage