How to run bandage with Trycycler fasta output?

Question

[greyman]

I have a bacterial genome that was deep sequenced and reached almost 100 percent of completeness (post Trycycler and medaka). Is there a way to generate or convert them into gfa format so I can view them in bandage? I tried SibeliaZ but the requested MAF alignment file that SibeliaZ created produces no output, maybe because there is only one input... Any suggestion? Anyone manually produce the gfa file before?

[andres.firrincieli]

Trycycler should output a gfa file for your assembly.

[greyman]

Hi andres, do you mean 5_chunked_sequence.gfa ? Shall I concatenate all of them from different clusters before loading into Bandage? But in that case I missed out from the final consensus data right? Thank you!

[andres.firrincieli]

Shall I concatenate all of them from different clusters before loading into Bandage?

Not sure if concatenating them will mess up the gfa file. You can try.

Ideally, you should get one cluster per replicon (one gfa per replicon) but keep in mind that the resulting gfa file will not represent the final assembly (consensus assembly).

But in that case I missed out from the final consensus data right?

You get a gfa file for each cluster generated by trycycler cluster but not from trycycler consensus which is the module used to generate a consensus contig sequence for each cluster

[greyman]

I tried to concatenate all gfa but the visualization in Bandage showed many short contigs in a single circular chromosome, I guessed thats what the chunked gfa output looks like. Is there a way to get the convert the consensus contig sequence from fasta to gfa? I thought that would be the whole point to do Bandage as to see the entire genome and contig distribution...

Big thanks!

[andres.firrincieli]

Is there a way to get the convert the consensus contig sequence from fasta to gfa?

I am sorry, but i am not aware of any method that can be used to get an assembly graph (gfa) from a fasta file. Check how trycycler works