Closed Rahimlou closed 1 year ago
Hello @Rahimlou,
Thanks for your interest in MetaCoAG.
If you check the contig names in the final.contigs.fa
file produced from MEGAHIT, the names will look something like the below.
>k141_31406
...
>k141_141323
...
>k141_565277
...
The value after k
will be the final k-mer size used by MEGAHIT to get the contigs. Then you can use this value for contig2fastg
to generate the .fastg
file.
Hope this helps.
Thank you!
Hi @Rahimlou,
Can you please let me know if your problem was solved, so I can close this issue?
Thank you!
Closing issue due to inactivity. Please reopen the issue if the problem persists.
Hello,
megahit_core contig2fastg accepts only a certain kmer (for example k=119) to write the fastg file. Which kmer size should I use to do this? Is there a way to get fastg file from the final contigs?
The syntax is as follows: megahit_core contig2fastg 119 intermediate_contigs/k119.contigs.fa > k119.fastg