Canu Assembly: BAM input file?

Question

[wlorenz]

I've been doing some test bacterial assy. running Canu ver 1.6 on some Sequel data. All works fine with extracted fastq or fasta data, but it fails if I try to pass the subreads.bam file- even though the program sees and begins the correction process before dying.

Should I be able to pass the subreads.bam or is this verboten? I have more detailed info. on script and errors to share, if this is an approach that one should be able to take.

Answer 1

[colindaven]

You can use a tool like bamtofastq to extract reads and pass these in. I'm not sure if BAM is an allowed input these days, but I don't think so.

bamtofastq filename=m54055_170517_074454.subreads.bam > 1K2_dig_subreads.fastq

You can find this in biobambam, available via bioconda.