Closed jarrodscott closed 2 years ago
OK. I think I answered my own question :) The final k*.contigs.fa
file is the assembly so I can generate a fastg
file from that, convert it to .gfa
, and then use the final assembly file to run MetaCoAG. Sorry for the confusion but I think I understand.
Hello @jarrodscott,
I'm extremely sorry for getting back late to you. The MEGAHIT assembly should result in the final contig file as final.contigs.fa
. You can use this file to get the assembly graph using the following command.
megahit_core contig2fastg 141 final.contigs.fa > final.fastg
MetaCoAG can run on the assembly from any k
value by generating the assembly graph from the contig files of the relevant k
value. However, the quality of the assembly may affect the binning.
Hope this helps. Let me know if you have any further questions. Your input and suggestions are highly appreciated.
Best regards, Vijini
Hi there!
I had a question about using
MEGAHIT
assemblies withMetaCoAG
. In theMetaCoAG
README it gives the following example:megahit -1 Reads_1.fastq -2 Reads_2.fastq --k-min 21 --k-max 77 -o /path/output_folder -t 8
I am using
--presets meta-sensitive
which sets the parameters to--min-count 1 --k-list 21,29,39,49,...,129,141
. Great. The instructions then say to run this on afastg
file.fastg2gfa final.fastg > final.gfa
So I need a
fastg
file from the MEGAHIT assembly. As I understand it, to get afastg
file from a MEGAHIT assembly, I need to runmegahit_core contig2fastg
, however the input for this command is not the final assembly but instead one of the intermediate kmer contig files in theintermediate_contigs/
directory. The help file for this command sayscontig2fastg convert MEGAHIT's k*.contigs.fa to fastg format
As an example you run it like so:
megahit_core contig2fastg 141 k141.contigs.fa > k141.fastg
My question is, in order to run
MetaCoAG
, does the agfa
(generated fromfastg
file) need to come from the final assembly file? If so, how can I generate afastg
from the final assembly file?Thanks!!