Hello all. I have done a plasmidSPAdes run on my bacterial reads to look for any plasmids. In the final output directory, I have the contigs.fasta file which contains the plasmids with the suffix componenet_X denoting each respective plasmid.
When looking at the different kmer value folders the K21-K99 folders seem to contain assemblies of the bacterial contigs in the final_contigs.fasta file, as a normal SPAdes run would. However, the K127 folder final_contigs.fasta is instead similar to the contigs.fasta file mentioned above - it seems to only contain plasmids and not the bacterial contigs.
After comparing the K127 final_contigs.fasta and contigs.fasta files with diff, they have differences. My question is why are these two files different? Is the contigs.fasta file different because SPAdes ran the mismatch corrector? And also why are plasmids only output in the K127 folder final_contigs.fasta and not the other kmer value folders?
Thanks
When looking at the different kmer value folders the K21-K99 folders seem to contain assemblies of the bacterial contigs in the final_contigs.fasta file, as a normal SPAdes run would. However, the K127 folder final_contigs.fasta is instead similar to the contigs.fasta file mentioned above - it seems to only contain plasmids and not the bacterial contigs.
After comparing the K127 final_contigs.fasta and contigs.fasta files with diff, they have differences. My question is why are these two files different? Is the contigs.fasta file different because SPAdes ran the mismatch corrector? And also why are plasmids only output in the K127 folder final_contigs.fasta and not the other kmer value folders?
Thanks
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