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Hi everyone,
I'm working on a project - Analysis of the genome of a probiotic bacterium to support commercial development. I need help determining if the gene classes may be beneficial or detrimental to the strains used as a probiotic.
For the overview of the project, I received 2 short read sequences (Illumina) and 1 long read sequence (Nanopore) and need to see how to get the best assembly using the data, either long and short together or just short, just long. After that, I did the Unicycler assembly and then ran a tool (Kraken2) to identify its bacteria name which is Pediococcus pentosaceus SL4. I also ran it with RAST to annotate my assembly and had a result https://docs.google.com/spreadsheets...it?usp=sharing
So my problem is how I could look at this RAST result to determine what genes P. pentosaceus does or doesn’t have that may influence its suitability for use as a probiotic. If there are more online tools to analyze it, can you be specific about what should I run?
Feel free to leave a comment, I really need help.
Thanks.
P/s: to clarify which tools ara used, they are from Galaxy Platforms (https://usegalaxy.org.au/)
I'm working on a project - Analysis of the genome of a probiotic bacterium to support commercial development. I need help determining if the gene classes may be beneficial or detrimental to the strains used as a probiotic.
For the overview of the project, I received 2 short read sequences (Illumina) and 1 long read sequence (Nanopore) and need to see how to get the best assembly using the data, either long and short together or just short, just long. After that, I did the Unicycler assembly and then ran a tool (Kraken2) to identify its bacteria name which is Pediococcus pentosaceus SL4. I also ran it with RAST to annotate my assembly and had a result https://docs.google.com/spreadsheets...it?usp=sharing
So my problem is how I could look at this RAST result to determine what genes P. pentosaceus does or doesn’t have that may influence its suitability for use as a probiotic. If there are more online tools to analyze it, can you be specific about what should I run?
Feel free to leave a comment, I really need help.
Thanks.
P/s: to clarify which tools ara used, they are from Galaxy Platforms (https://usegalaxy.org.au/)