Understanding kmer contigs for FASTG Output

voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler

http://www.ncbi.nlm.nih.gov/pubmed/25609793

GNU General Public License v3.0

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Understanding kmer contigs for FASTG Output #323

Open joshuakirsch opened 2 years ago

joshuakirsch commented 2 years ago

Hi,

Thank you so much for this great tool. I was hoping to use Megahit to build fasta graphs for input to SCRAPP ([https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01068-z]). From reading your tutorial on converting the contigs into FASTG, I am confused on which kmer size to use for input. If you could please enlighten me on whether I should use high or low kmer contigs or some other input when you have a chance, I would greatly appreciate.

Thanks!

thaumP commented 2 years ago

Have you solved this problem? I have the same confusion

chiaramazzoni commented 2 years ago

Hi, I was also thinking about doing the same, I noticed that in final.contigs.fa (in the contig names) it's reported from which k-mer size your contigs were selected from (not sure if it's always the highest) so I guess that would be the one to investigate if you want to visualize your final assembly...