No output for two WGS analyzed... about smashpp

[pratas]

Dear Frank,

I think smashpp is not completely prepared to handle FASTQ but rather FASTA only.
Perhaps assembling first the genome will work.
Perhaps the image is not generated because the minimal block size must be lower than the FASTQ read size (DNA sequence). For example, try 80.

Best regards,
Diogo

[frankMusacchia]

Thank you, Diogo, for your answer. I will let you know how it goes with 80. How do you usually assemble wgs for smashpp? Is Velvet good, for example, or you suggest any other tool/pipeline? Best regards Francesco

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Il giorno 4 set 2021, alle ore 14:57, Diogo Pratas ***@***.***> ha scritto:  Dear Frank, I think smashpp is not completely prepared to handle FASTQ but rather FASTA only. Perhaps assembling first the genome will work. Perhaps the image is not generated because the minimal block size must be lower than the FASTQ read size (DNA sequence). For example, try 80. Best regards, Diogo — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

[pratas]

Dear Frank,

For assembling it depends on the genome type, sequencing process/protocol, and may other things. Assembling a genome for one type may not be necessary the best way to another purpose. For viral enriched genomes, we use TRACESPipe ( https://github.com/viromelab/tracespipe ). TRACESPipe combines both de-novo (metaSPAdes) and reference-based assembly (bowtie2) through iterative refinement for multi-organ sample purposes. However, if you want to assemble other types of genomes , for example humans or plants, you may want to check assemblers such as Hifiasm (there are many others) and combine sequencing long reads with short reads.

Best regards,
Diogo