rrwick
getting multiple contigs along with complete circular genome
i have sequenced a genome using nanopore MINIon. the basecalling was done using guppy software. After assembly done using unicycler by running following command unicycler -l /home/pbp/Documents/run7/run7_filtered/PSHaemo3_2kbfiltered.fastq -o /home/pbp/Documents/run7/PSHaemo3_assembly --mode bold The assebly.gfa file was visualized in bandage and in addtion to circular genome, am getting around 37 small linear fragments along with five plasmids. how do i get just the circular genome and plasmid without these linear fragments.
Using Bandage, you can select the segments with their numbers or clicking and selecting them from the visualization, then clicking in the Output menu tab at the top of the window and selecting to export the selected paths as FASTA or as clipboard.
Worth noting that assembly.gfa includes smaller contigs (>100bp) that are not present in assembly.fasta - details here.
