Question about Mira parameters

Question

[gustavojorge080]

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?

[Sej Modha]

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.

[gustavojorge080]

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.

[gustavojorge080]

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!

Answer 1

[gayachit]

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?

[gustavojorge080]

Hello.

The readings were sequenced on the ION PGM platform.