Labelling sequences for paired-end assembly using Mira ?

[Yves]

Hello,

Just have a question for Mira assembler. I would like to assemble paired-end Illumina data but i don't know what sort of labelling is required.
It seems that adding /1 and /2 at the end of the head is the key, but the Mira guide don't give out any more informations . I am just wondering, in my case if something else is not necessary :

Here are the head of paired-end sequences :

@HWI-ST909:120:C0NW7ACXX:5:1101:1343:1979 1:N:0:CTAGGC

@HWI-ST909:120:C0NW7ACXX:5:1101:1343:1979 2:N:0:CTAGGC

The question is : should I parse the heads like this :

@HWI-ST909:120:C0NW7ACXX:5:1101:1343:1979 1:N:0:CTAGGC /1

@HWI-ST909:120:C0NW7ACXX:5:1101:1343:1979 2:N:0:CTAGGC /2

or like this ?

@HWI-ST909:120:C0NW7ACXX:5:1101:1343:1979 1:N:0:CTAGGC /1

@HWI-ST909:120:C0NW7ACXX:5:1101:1343:1979 2:N:0:CTAGGC /2

Thank you very much for your help !

[maubp]

You can try MIRA 3.9.x (the development series) which understands the new naming convention.

For MIRA 3.4.x (the current stable release) the /1 or /2 needs to be on the end of the identifier (i.e. the first word, BEFORE any spaces). i.e. In this example,

@HWI-ST909:120:C0NW7ACXX:5:1101:1343:1979/1 1:N:0:CTAGGC

@HWI-ST909:120:C0NW7ACXX:5:1101:1343:1979/2 2:N:0:CTAGGC

or:

@HWI-ST909:120:C0NW7ACXX:5:1101:1343:1979/1

@HWI-ST909:120:C0NW7ACXX:5:1101:1343:1979/2

should be fine.

[Yves]

Thank you so much !