Julian Garneau

Hello Ruby, thanks for your message, If you aggree, could you send me your PhageTerm report, so I can have a look at the coverage on your assembly? PhageTerm has been developed and tested for randomly sheared short reads. We haven't tested officially with long reads, so we can't be sure that it will work or not. In principle , if the quantity of reads starting at the termini is really high, and reads starting randomly over the genome is well distributed everywhere on the genome, we expect phageterm...

Hi Melissa, thanks for your message, It is hard for me to give a decisive answer on this case, but yes, PhageTerm is usually conservative and will not suggest the re-organization it there is an uncertainty with multiple termini. I would have to look at the report to have a better idea of what is happening there... If you want to send me your report I can have a look: julian.garneau@unil.ch Cheers, Julian

Hello, thanks for your message, You have a phage genome from ONT, are you talking about the assembly? Do you have short reads from Illumina sequencing or you only have long read from ONT sequencing? Thank you

Hi again Concha, Could you send me an e-mail at julian.garneau@pasteur.fr WIll be easier to exchange on there, Thanks!

Bonsoir :) When you run the installation test, could try without your own reads, as follow : $ /home/user/software/phageterm-1.0.12/PhageTerm.py -t C5 Tell me if this command works properly on your system. If not, maybe you should force launching phageterm with python2 : $ python2 PhageTerm.py -t C5 And with your own reads : $ python2 PhageTerm.py -f K10PH82C1_S15_R1_001.fastq -p K10PH82C1_S15_R2_001.fastq -r K10PH82C1_sequence.fasta -n K10PH82C1 -c 4 Keep me posted if it worked with one of those...

Hello, Please tell me more about the results. What type of phage have you got in the PDF report? I ask because a fasta file is not generated for all types of phage. (If your phage is type T4 with no precise termini, we cant generate a fasta file reorganized to start at the termini because there is no termini). So the absence of a fasta file is not necessarily a bug. But I need more info to know if its a bug here or not. Thank you :)

Hi Gustavo, thanks for the details, I forgot to ask you, what procedure did you use to sequence your phage? Did you do illumina TruSeq libraries? Nextera? Other? For further communications, do you mind writing me on my email ? This will be faster and easier :) At: julian.garneau@pasteur.fr

Hi again Gustavo, Can you help me by telling me what is the result you obtained on that contig after the PhageTerm analysis? That should help me help you. Only thing I can guess for now, is that your result is possibly a "DTR-long" , and that the repeat region was taken out of the reorganised genome. However, since there is a 21 503 difference between both contigs, that seems pretty big for a DTR, which I think at maximum have been seen at around 10 000 bp. But that is not impossible. Anyway, I will...