I recovered an N amount of putative chloroplast contigs (fasta format). I need to align them to a reference genome and there is no reference genome of my species. Fortunately, there is a reference genome of the same genera. So, I think I should align the contigs as if they where homologous sequences of the reference. I have tried using bowtie2 (--very-fast-local option) but I end up loosing a lot of information, and when I use Blastn, almost every contig hits with my reference.
The final goal is to obtain an inferred chloroplast for my species.
May someone suggest me a workflow/article to read in order to achieve this objective?
In a few words, I need to construct a genome from a close reference and putative homologous sequences.
Use the MUMMER package to align your contigs with the reference. Then use the MUMmerplots R package to visualize the alignments.
Thank you very much, Mark Farman!
I solved this issue using RagTag:
Article RaGOO: Fast and accurate reference-guided scaffolding of draft genomes
As the description in the git says, "is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome". And it worked fantastically. At this moment I am only trying to recover some contigs to obtain the best from the scaffolding process.
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