Unicycler

[szy0931]

I know Unicycler is specialised for bacterial genome assembling from hybrid of short and long reads.
But, is Unicycler also good for bacterial genome assembling only from short reads such as from Illumina MiSeq

[Bukowski]

Yes, because it acts as an optimiser for Spades.. which is perfectly happy with just short read data.

[szy0931]

Thak you very much!
I have one set paired (2 x250) Illumnia MiSeq data from Salmonella.
They look good by FastaQC
I did Unicycler assembling but I did not get a whole genome.
The longest contig is 446213 and totally I got 59 contigs longer than 500 bp.
What can I do next?

[Bukowski]

Some minION sequencing?

There's nothing wrong with that number of contigs from a 2x250 MiSeq run.