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Old 04-02-2012, 11:50 AM   #1
foeckingmf
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Default MIRA assembler hybrid assembly -Filenames?

Hello. I'm trying to use MIRA to do a hybrid assembly of 454 and Illumina reads. It's not clear from the manual how one tells the program which files are which. Can it automatically identify the sequencing technology? Are there examples anywhere of the command line for a hybrid assembly?

Also, can the program be run from a text file containing the command lines? I'd like to save what I do because I don't do this very often :-)

Thanks for any info.

Mark
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Old 04-02-2012, 12:56 PM   #2
krobison
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I assume you are on a Linux system; in that case you can save the command to a shell script (typically with a file extension .sh)

http://mira-assembler.sourceforge.ne...ence_part.html -- look in the section 5.3.14 -FILENAME. The standard naming convention is

<projectname>_in.<seqtype>.fastq

So, if you had Sanger & Ion Torrent data for a tribble sequencing project, it would have files

tribble_in.iontor.fastq
tribble_in.sanger.fastq
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Old 04-03-2012, 04:39 AM   #3
foeckingmf
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Thank you. I did just run across that and I'll try it. Lot of pages in those docs. I am on a Linux system and the shell script should have occurred to me (I'm much more of a wet bench guy than a computer guy).

It looks like a really versatile program, but one with a long learning curve...

Mark
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