Contig assembly

Ashu · 03-07-2011, 11:51 AM

Hi everyone,
Can someone enlightened share his/her knowledge about how I can merge the contigs from different assembly outputs.
I have seen CAP3, MIRA ... I would be very happy if you can just give me a summery of the tools.
Thank you
Ashu

boetsie · 03-08-2011, 01:48 AM

Hi Ashu,

you can have a look at this thread;

http://seqanswers.com/forums/showthr...ighlight=merge

also ken kraaijeveld has some suggestions;

http://www.kenkraaijeveld.nl/genomics/bioinformatics/

What you can also do is cut all the contigs into 'reads', including some overlap, and do a new de novo assembly (with your favorite program) with these reads. You could use for example the perl program from nagarjun (breaks down the contig into 1000bp reads with 500bp sliding window);

http://nagarjunv.blogspot.com/search...max-results=34

For small contigs, you could probably better use smaller window size and smaller reads... A good de novo program for this would be something like SSAKE or Abyss, at least some program were you can specify your minimal coverage. This setting depends on if you want to do an "intersection" between the contigs, or an "union".

Kind regards,
Boetsie

Ashu · 03-08-2011, 05:00 AM

Thank you very much Boetsie, I will check them all,
Wishing you a good day,
Ashu

boetsie · 03-08-2011, 05:16 AM

You are welcome, good luck and good day to you too

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03-07-2011, 11:51 AM	#1
Ashu Member Location: NL Join Date: Aug 2010 Posts: 15	Contig assembly Hi everyone, Can someone enlightened share his/her knowledge about how I can merge the contigs from different assembly outputs. I have seen CAP3, MIRA ... I would be very happy if you can just give me a summery of the tools. Thank you Ashu

03-08-2011, 01:48 AM	#2
boetsie Senior Member Location: NL, Leiden Join Date: Feb 2010 Posts: 245	Hi Ashu, you can have a look at this thread; http://seqanswers.com/forums/showthr...ighlight=merge also ken kraaijeveld has some suggestions; http://www.kenkraaijeveld.nl/genomics/bioinformatics/ What you can also do is cut all the contigs into 'reads', including some overlap, and do a new de novo assembly (with your favorite program) with these reads. You could use for example the perl program from nagarjun (breaks down the contig into 1000bp reads with 500bp sliding window); http://nagarjunv.blogspot.com/search...max-results=34 For small contigs, you could probably better use smaller window size and smaller reads... A good de novo program for this would be something like SSAKE or Abyss, at least some program were you can specify your minimal coverage. This setting depends on if you want to do an "intersection" between the contigs, or an "union". Kind regards, Boetsie Last edited by boetsie; 03-08-2011 at 01:58 AM.

03-08-2011, 05:00 AM	#3
Ashu Member Location: NL Join Date: Aug 2010 Posts: 15	Thank you very much Boetsie, I will check them all, Wishing you a good day, Ashu

03-08-2011, 05:16 AM	#4
boetsie Senior Member Location: NL, Leiden Join Date: Feb 2010 Posts: 245	You are welcome, good luck and good day to you too