Chris Fields

@mgabriell1 note that @benjjneb just released a new error model for binned quality data in the master branch, might be worth a try

Seeing the same, but using `mashmap` PAF. It looks like a parsing bug. The first few lines in the `mashmap` PAF I'm using: ``` atg000001l 43020 0 43020 - Ms71#1#chr5...

@zmughal Does PDL (or the Perl community in general) have a minimum recommended version to support? I'd say go with that for support and testing purposes. Perl 5.8 was the...

Thanks for running that @zmughal. I vote we go with the minimum Perl version from the runtime analyses, Perl 5.12 is just over 13 yrs old (2011). Not that it's...

@emankhalaf just a note: ``` #SBATCH --time=0-48:00 #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1 #SBATCH --cpus-per-task=1 #SBATCH --mem-per-cpu=200000M ``` This will run single-threaded, which can take a very long time and (depending on...

> Thanks@cjfields for your input. Do you have any idea how can I use 200GB memory total? On our cluster we use `--mem 200g`. In a batch script (4 cores...

> In your example, you likely used the PacBio Ultra Low Input library (based on these results and the apparent PacBio SMRTbell blunt adaptor contamination) which has some shared subsequences...

@trawler-crawler would these be from Kinnex kit data by any chance? I've seen this pattern before (what effectively looks like two separate curves).

@emankhalaf see #1892, but note that @benjjneb recently added a new function for dealing with binned quality scores on the 'master' branch. I have found processing any Revio data (especially...

Just so there is record of this: we find PacBio Kinnex samples take considerable resources even when using binned reads, likely due to the ~15x increase in yield for a...