MIRA assembly error

Question

[glady]

Hi, I am uploading a job on MIRA. I want to assemble a bacterial genome, I have created a manifest file with all the desired features (denovo, paired end sequencing, Illumina, etc). But, while running MIRA it is giving me an error that the coverage size is exceeding beyond 300x. How can I takle this issue? How can I cut down the coverage size of my data?

[GenoMax]

You could downsample the reads (if you truly have a lot) by using reformat.sh from BBMap suite.

To sample 10% of the reads:
reformat.sh in1=reads1.fq.gz in2=reads2.fq.gz out1=sampled1.fq.gz out2=sampled2.fq.gz samplerate=0.1

or more concisely:
reformat.sh in=reads#.fq.gz out=sampled#.fq.gz samplerate=0.1

and for exact sampling:
reformat.sh in=reads#.fq.gz out=sampled#.fq.gz samplereadstarget=100k

[glady]

After running BBMap, then should I upload those output files to MIRA as input ? Will doing this solve the problem of coverage ?

[GenoMax]

Is the coverage size error referring to size of the total input sequence data? If yes, then the solution above would allow you to sample the data down to a size you want/need.

BTW: What is the expected genome size and how much raw data do you have?

SPAdes is in general a better option for assembling bacterial genomes.

[glady]

I have used SPAdes already, but it generated a lot of contigs, more than 4000.

[vmicrobio]

I used a lot MIRA and SPAdes for bacterial genomes (MIRA generates often less and taller contigs for me) and never have this error. You may ask by email directly to Bastien Chevreux