Antonio Fernandez-Guerra comments

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                                            Antonio Fernandez-Guerra

Using already predicted ORFs from reads

Thanks Martin! I have a couple of hundreds of metagenomes to assemble. For now, I will try to modify the PLASS assembler workflow and add these steps and see if...

Using already predicted ORFs from reads

Hi Martin I modified [assembledb.sh](https://github.com/soedinglab/plass/blob/master/data/assembledb.sh#L29-L65) to include the hack you suggested and seems to works correctly. I can reduce the number of assembled proteins with the default NN filter value....

Incorrect headers for Nuc -> Protein

Hi Martin any news on the issue? Thanks Antonio

Incorrect headers for Nuc -> Protein

Thank you very much @AnnSeidel! The coverage field will be very useful when added! Regarding the nucleotide assembly, is it still considered experimental?

Unbiased DFA

@stfbnc Many thanks! 😀

Unbiased DFA

That is excellent, @stfbnc! Thank you very much, and apologies for the radio sile; it has been a time of grant submissions :tired_face: That will be super useful :smiley:

HIBF creates a very large index

Hi @eseiler thank you very much for your prompt answer, it is very useful. I will try your recommendations :-) You can get the genome fasta files from [here](http://files.metagenomics.eu/gtdb-hires-v6.tar) and...

HIBF creates a very large index

An update on this, without specifying `--determine-best-tmax` now the index is only 588GiB and the peak memory has been 590GiB

SAM file formatting

@milot-mirdita, we are also interested in the SAM formatted output for translated searches. In our use case, we would like to get a nucleotide output. Many thanks!