Question: Question about Mira parameters
0
gravatar for gustavojorge080
12 months ago by
gustavojorge08010 wrote:

Hello people.

I am using the Mira assembler in some iontorrent readings. What is the difference between the min_length and minimum_read_length parameters in the MIRA assembler?

ion iontorrent mira assembly • 272 views
ADD COMMENTlink modified 11 months ago by gayachit200 • written 12 months ago by gustavojorge08010
1

According to the manual: http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.pdf

[min_length(ardml)=integer > 1] Default is dependent of the sequencing technology, currently 400 for Sanger and 200
for 454 and Ion Torrent.
A coverage must be at least this number of bases higher than [-AS:ardct] before being really treated as repeat.

[minimum_read_length(mrl)=integer ≥ 20] Default is dependent of the sequencing technology. Defines the minimum
length that reads must have to be considered for the assembly. Shorter sequences will be filtered out at the beginning of
the process and won’t be present in the final project.
ADD REPLYlink written 12 months ago by Sej Modha4.8k

Many thanks for the reply.

What value would you give me for the parameter "minimum_read_length" with iontorrent type readings.

Ps: This information is not in the manual.

ADD REPLYlink written 11 months ago by gustavojorge08010

Hi guys. Its me again.

Could someone explain to me how the parameter "kmer_series (kms)" works? What does "number of passes " mean? I could not understand the explanation of the manual.

What value would you recommend me to use for this parameter?

Thank you very much in advance!

ADD REPLYlink written 11 months ago by gustavojorge08010
0
gravatar for gayachit
11 months ago by
gayachit200
India
gayachit200 wrote:

Hi

For Ion Torrent your minimum read length depends on the chemistry used for sequencing (which could be 200 bp or 400 bp). You must have got summary report which gives you an idea of mean read length and minimum length. Parameters should be given keeping that in mind. Is this an Ion PGM run or Ion Proton run or Ion S5?

ADD COMMENTlink written 11 months ago by gayachit200

Hello.

The readings were sequenced on the ION PGM platform.

ADD REPLYlink written 11 months ago by gustavojorge08010
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