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.