[wgs-assembler-users] PGM, multithreading and default settings

[Sebastian J. <jue...@Ce...>]

Hi everybody,

i want to use CELERA to assemble data from different platforms (PGM, 
MiSeq, GS Junior) independently and i'm a bit confused about how to set 
the parameters right.

First off, does anyone already have experience using CELERA and Ion 
Torrent PGM data? I would suggest to treat PGM data as 454 data in terms 
of parameters but some shared experience could help. Also, as PGM 
provides sff files i would like to know if CELERA is capable to handle 
PGM based sff files or if i better should fastq exports.

Next, which options should be set to which values in order to run CELERA 
in a non-grid parallel environment. Say i do have a single machine 
having 12 CPUs (sockets) each consisting of 4 cores and i want that each 
consecutive step of CELERA is using all 48 cores. Is there one single 
option for that or do i have to set all *Threads options individually 
(e.g. 'ovlThreads=48', 'mbtThreads=48' etc.). Also, are all those steps 
for which a thread number can be given really executed consecutive? 
Regarding the memory consumption, are all *Memeory settings (as e.g. 
'merylMemory') process based? If so it's crucial to know, because if 
relying heavily on multithreading the memory should be raised 
accordingly. Would be something like memory=number_of_threads*400MB a 
good rule of thumb estimate for those settings?

There are also a lot of other options for which i could not find any 
useful recommendation or documentation. Do i have to set all those >150 
options in order to get good results or does CELERA have good default 
values based on the input data. This confusion already starts at what 
overlapper and unitigger should i use for PGM and MiSeq (ovl, mer, umd 
and utg, bog, bogart)? Where are the main differences? Does CELERA 
determine the input type based on the filename or on the type given when 
converting to FRG format (-type).

I know these are many questions but there also a lot of settings that 
can be altered tweak, so i hope forgive me.

Tanks,

Sebastian

-- 
Sebastian Jünemann
CeBiTec - Center for Biotechnology
Bielefeld University, D-33594 Bielefeld, Germany
Office: V6-147 -- Phone: +49-(0)521-106-4827	
eMail: jue...@Ce...