[mira_talk] Re: MIRA edits reads during assembly?
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 25 Oct 2009 11:44:39 +0100
Hi Bastien,
On 25 Oct 2009, at 11:15 , Bastien Chevreux wrote:
let me start with an old citation: "Ceterum censeo, ACE esse
delendam."
I do agree. But before there is another program to replace consed to
finish assembly, or that consed developers change the format, I don't
see any other issue than to find workarounds. Gap5 looks promising,
but feature-wise, it's still far from reaching the level of consed...
By the way, have you heard about ABySS-Explorer? There was a paper in
TVGC recently. Haven't seen the program at work yet, but it looks nice
(http://www.computer.org/portal/web/csdl/doi/10.1109/TVCG.2009.116).
Again, it's far from being a finishing program, but the graphical
representation is quite interesting.
I hope that with "change" you mean: some are deleted. Other changes
shouldn't
be.
Some bases are deleted in some reads, yes. Couldn't detect any other
changes, indeed.
For 454 and Solexa reads, I wrote a much simpler editor which look
for common
overcall problems which it can safely delete. There's a whole set of
rules
behind it, but basically this editor wants a certain base to gap
ratio,
forward/reverse reads and a few things more before it decides to
edit away a
base in a read.
OK, good to know...
Thanks for the answer! Parsing the reads from the caf files wasn't
hard anyway. But for the sake of the poor souls that still use the
damned ace format and consed, may I suggest that it might be
interesting to have the possibility to output a phdball with
convert_project?
Cheers,
Lionel
(Guy is actually my last name... know it's confusing given the email
address)
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
