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Old 10-14-2009, 01:41 AM   #1
edge
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Default Discussion about MIRA hybrid assembly of 454 reads with Illumina unpaired data

I got a 454 file named as Read.454.fasta and another two more file named as Illumina_unpaired_read.solexa.fasta and Illumina_unpaired_read.solexa.fasta.qual
How should I do or type to let the MIRA program to the hybrid assembly of these 454 reads with Illumina reads.
I got read the this manual:
http://www.chevreux.org/uploads/medi...solexadev.html
Unfortunately, it can't help me a lot to solve my problem.
Thanks a lot for all of your help and explanation. Kindly told me if I still need other extra info_file for MIRA to run properly.
Thanks again
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Old 10-16-2009, 06:13 PM   #2
edge
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I feel a bit confusing by using MIRA's "De-novo hybrid assemblies".
For example, I got a bacteria genome which sequencing by 454 technique and Illumina technique separately.
After run 454 reads by using MIRA and BAMBUS, I extract the longest scaffold and treat it as a backbone. I hope that I able to polish this longest scaffold by using Illumina reads to get better assembly result.
I just confusing how to use MIRA to polish my longest scaffold and get better assembly result.
Thanks again for everybody.
Hope that who experience or familiar at MIRA can help me solve my troubles.
Kindly to remind me if I have done any mistakes when deal with MIRA to De-novo hybrid assemblies.
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Old 11-09-2009, 05:38 AM   #3
Mira
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I also try to assemble a relatively small bacteria genome by using de-novo hybrid assembly (454 and Illumina). Unfortunately it seems that the program (or the computer) is overloaded with 3.5 mio reads (Illumina - 36bp each) and 45.000 reads of 454. Normally the computer works well, so I am searching for the mistake. What can I do? Any ideas?
Thanks in advance,
Mira
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Old 11-10-2009, 12:14 AM   #4
sklages
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What is "overloaded", what is "normally" and what is "the computer"? This is not very specific for troubleshooting ;-)

Sven
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Old 11-10-2009, 04:40 AM   #5
Mira
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Thank you for the quick reply
I have a computer running with linux (64 bit), 4 GB RAM and additionally 8 GB SWAP. It took less than 24 hours with 1.6 million reads of illumina and 47.000 of 454. I guess the processing time mainly depends on the number of illumina reads. Maybe I am a bit impatient. I am really looking forward to the results. Do you have any idea how long it will take with the same amount of 454 reads, but approx. the double amount of illumina reads?
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Old 11-16-2009, 01:17 AM   #6
Mira
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Hey,

now I have the answer. It took appr. 3 days.

Anyway, thanks a lot.
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