So, first time attempting to use quiver to polish an assembly I created in Canu. All of the software is installed and functional via command line (quiver, pbalign, bax2bam, quiver, arrow, etc). Our systems people installed using pitchfork.
I have the assembly in .fasta format and I also have 30ea bax.h5 files to utilize. The issue comes when I start looking at blasr which apparently no longer outputs cmp.h5 files that are preferred by pbalign. blasr now defaults to .bam files (nice for standardization I guess) and it isn't obvious that pbalign will utilize .bam as input. Found this little snippet which was somewhat informative:
Ultimately, in short, I simply want to utilize the bax.h5 files with quiver (or arrow) to polish the assembly I did in Canu.
I have the assembly in .fasta format and I also have 30ea bax.h5 files to utilize. The issue comes when I start looking at blasr which apparently no longer outputs cmp.h5 files that are preferred by pbalign. blasr now defaults to .bam files (nice for standardization I guess) and it isn't obvious that pbalign will utilize .bam as input. Found this little snippet which was somewhat informative:
Ultimately, in short, I simply want to utilize the bax.h5 files with quiver (or arrow) to polish the assembly I did in Canu.
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