contig2fastg

[Rahimlou]

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

[Vini2]

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!

[Vini2]

Hi @Rahimlou,

Can you please let me know if your problem was solved, so I can close this issue?

Thank you!

[Vini2]

Closing issue due to inactivity. Please reopen the issue if the problem persists.