[Champi]

For the same coverage in high quality reads will the input amount in raw reads affect the correction? Does pacbioToCA correct raw reads independently?

I typically run with a single fastq from 2-4 filtered SMRTcells with 50X-100X of high quality correction reads followed by assembly.

I don't really understand what you mean by "high quality correction reads". One thing is the quality: the per-position-quality in a read can be good, but it does not mean that the nucleotide placed there by the PacBio polymerase is the correct (actually it achieves ~80% accuracy). You have to correct the filtered reads (those with length and quality good enough, filtered usually by your provider) using either Illumina (or other) or, if you used C2 technology for your PacBio sequencing, the filtered reads themselfs.

For the latter, you can follow this tutorial:

http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA#Self-Correction_With_C2_Sequences_.28or_newer.29

[sdsouza3]

No fasta file from pacBioToCA

So I resolved the run time issue for my data with the pacbio spec file you posted, but I only get a .frg file out from my pacBioToCA correction (no .fasta or .qual). I'm assuming it has finished doing its thing? I find it really peculiar that I'm not getting the other output files. Any thoughts as to what might be going on?

Related question: which subdirectories does pacBioToCA create? Sometimes it skips making the 0-mercounts directory and sometimes it doesn't...

(For the assembly I've just put in the .frg file that came out of pacBioToCA and I'm going to see what comes out of celera and check if something weird is happening from that.)