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rrwick / Unicycler

hybrid assembly pipeline for bacterial genomes
GNU General Public License v3.0
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trying to circularize a bacterial genome #211

Open katavalderrama opened 5 years ago

katavalderrama commented 5 years ago

Hi, I'm trying to sequencing the genome of a bacteria. I have the PacBio assembly that consists of one contig (I have another but it's for the plasmid); so, what I need is to circularize this sequence. The contig has a repeated sequence in the beginning and in the end, so I'm pretty sure that the genome is close, but I can not circularize this. I try to use Unicycler for long reads, but it gives me this error: "Error: you must use both --short1 and --short2 or neither"...

Any help? (I'm new with this!)

THANKS!

stevenjdunn commented 5 years ago

What command are you running? It should be something along the lines of: unicycler -l pacbio_reads.fastq.gz -o output_dir - it looks like you may be using the -1 or -2 flags somewhere in there.

You may also want to look into Circlator if you already have a single contig assembly.