Unicycler generating short contigs during hybrid assembly

Question

[hermoinejean]

Hi

I have been using Unicycler to assemble PacBio and Illumina reads for a set of bacteria genomes. For one of the organisms, when I run Unicycler with both types of reads, it generates an assmebly with total length 171 706 bp. If I run it with the long reads only, the total length is over 2.6 millon bp (much closer to the expected genome size). Anyone know what is going on here? I also assembled the same reads using Canu, and then aligned the Illumina reads to this assembly with BWA, and there does not seem to be any problem with the reads not aligning or anything like that.