influenza

[MuYi-Yang-cell]

Is your feature request related to a problem? Please describe. For generic questions use Q&A section in the Discussions forum above.

Hello,

I'm currently using SPAdes for de novo assembly of avian influenza virus genomes. The genome consists of 8 independent segments and was sequenced using Illumina NextSeq for paired-end reads (2x100). However, the scaffold results from the assembly are not as satisfactory as I hoped. I noticed that someone else had asked a similar question before. I've tried using the following parameters for the assembly. Is this the optimal parameter combination, or do you have any other suggestions? Thank you

python coronaspades.py --custom-hmms U-RVDBv20.0-prot-influenza.hmm.gz -t 8 -1 ../WA2308002_1.fq -2 ../WA2308002_2.fq -o Filter_SPAdes

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Additional context

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[asl]

Can you provide the spades.log file at least?

[MuYi-Yang-cell]

Okay, here is the log file from my run. My description might have been a bit unclear. I wanted to inquire whether this parameter configuration is the optimal one. If I were to include a reference genome, would it potentially improve the assembly results?

Spades.log

[asl]

Okay, here is the log file from my run.

The file is not complete, the run seems to be still ongoing? Also, it does not seems you're running coronaspades.py.

[MuYi-Yang-cell]

I apologize, this is the actual log file.

Spades.log

spades.log

[asl]

All right. Can you also upload hmm_statistics.txt from the output dir?

[MuYi-Yang-cell]

Sure, the file within this result folder hmm_statistics.txt

hmm_statistics.txt

[asl]

Ok, and assembly_graph_with_scaffolds.gfa as well, please

[MuYi-Yang-cell]

Right here. I've changed it to the TXT format because GitHub doesn't recognize GFA-format files.

assembly_graph_with_scaffolds.txt

[asl]

Ok, so there are 8 segments that are almost completely assembled. Why you're saying "not as satisfactory"? What is wrong?

[MuYi-Yang-cell]

Indeed, I have reviewed the scaffolds.fasta results, and this is the best outcome I have achieved after multiple attempts. My description might have been a bit unclear. Is this the optimal parameter combination, or do you have any other suggestions?

[asl]

This was exactly the way how the Influenza benchmark benchmark was performed in coronaSPAdes paper.

[MuYi-Yang-cell]

Yeah， Thank you for your response!