I have some plasmids (purified) that were 1x150 sequenced on Illumnia. I am trying to assemble them, but am not having success using SPAdes or tadpole.sh from BBTools (both have been suggested by others to assemble viral genomes which are comparable in size). I have plenty of coverage with the number of reads generated (1000+X coverage). SPAdes produces 1000 contigs with the longest one being 1,482 bases. tadpole.sh produced 19 contigs with the longest being 912 bases.
I feel like I am missing some parameters somewhere to get a better assembly.
Here is the SPAdes command:
spades.py --careful -s XXXX.fastq.gz -t 24 -m 31 -o SPAdes_assembly_XXXX
Here is the tadpole.sh command:
tadpole.sh in=XXXX.fastq.gz out=contigs_XXXX.fa k=93
Any suggestions on what parameters I should change to get a better assembly (i.e the full length plasmid in a single contig)?
Is there a special tool out there to do plasmid assemblies (I tried plasmidSPAdes.py too with no luck).
Any other information that would be helpful?