[mira_talk] Re: virus genome assembly
- From: Chris Hoefler <hoeflerb@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 22 May 2014 10:18:47 -0500
You cannot get 600 bp reads on a HiSeq, so the first thing you have to do
is understand what kind of data you have.
- What is the read length? On a HiSeq 100 bp is typical, but 150 bp is
also an option.
- Is it paired or unpaired data?
- If it is paired data, what is the library insert size? This is probably
where your 600 bp number comes from, but your sequencing provider should
have measured the distribution. Mira likes to know the minimum and maximum.
- If it is paired data, what is the orientation of the reads (innie or
outie)? For a typical paired-end experiment it is innie.
Strictly speaking, Mira can manage without the last two, but it is best to
give it as much information as you can. For the manifest file, you can grab
a good starting place from the Mira4 manual,
http://mira-assembler.sourceforge.net/docs/#sect_dn_mf_manifest_for_pairedend_data
http://mira-assembler.sourceforge.net/docs/#sect_ref_manifest_basics
On Thu, May 22, 2014 at 2:31 AM, Laurent MANCHON <lmanchon@xxxxxxxxxxxxxx>wrote:
> Le 21/05/2014 23:19, Bastien Chevreux a écrit :
>
> On 21 May 2014, at 22:00 , Laurent MANCHON <lmanchon@xxxxxxxxxxxxxx>
>> wrote:
>>
>>> Does someone has already used MIRA to assemble a viral genome (HIV type)
>>> using long reads(600bp) libraries ?
>>> An example of manifest file would be welcome…
>>>
>> Technology?
>>
>>
>>
> HiSeq
>
>
>
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