Question: MIRA for metagenome assembly
gravatar for Rahul Sharma
4.7 years ago by
Rahul Sharma600
Rahul Sharma600 wrote:

Hi all,

I am working on a de novo metagenome assembly project. In this data I am expecting several species of bacteria. The sequencing data I have received have been sequenced with Illumina 100-300 bp inserts with a read length of around 150 bps. I was giving a try to MIRA genome assembler, however there are around 150+ parameters to tune a assembly. I will be very thankful if anyone can share his/her experience with MIRA for metagenome assembly and how to optimize it for several closely related bacterial species within the sample. 

Here is how my manifest file looks like:

project = MyFirstAssembly
job = genome,denovo,accurate
parameters = -GE:not=4

readgroup = SomePairedEndIlluminaReadsIGot

data = datape*.fastq
technology = solexa
template_size = 100 300 autorefine
segment_placement = ---> <---
segment_naming = solexa

I would like to know if anyone have tested MIRA with some specific parameter for metagenomic data, where diversity is high and chances missing out is also high.
It would be very great if anyone can share an example manifest file.

Many thanks in advance! Best reagrds, Rahul
mira metagenome next-gen • 2.0k views
ADD COMMENTlink written 4.7 years ago by Rahul Sharma600

Mira relies heavily on the assumption, that the coverage along the whole genome is uniform/constant. If your DNA was harvested from a single organism or from a single bacterial colony, this assumption is true for most part of the genome. In metagenomics the genome consists of several chromosomes and plasmids. I doubt, that all of them are present in your sample with the same copy number. 

ADD REPLYlink written 4.7 years ago by piet1.7k
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