analysis method for pure samples of bacteria sequences

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Hello everyone,

I'm relatively new to the field of microbiome research and could use some guidance regarding a general question I have. I have a set of 15 samples consisting of pure bacteria sequences along a quality average score and length of contig for each sample sequence, and I'm interested in determining their respective phyla. I was wondering if someone could provide insight into the appropriate analysis and methods to accomplish this. Additionally, I would like to know if Qiime is a suitable tool for this task.

Any help or suggestions would be greatly appreciated!

Thank you in advance.

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Hi @gjahanmir,
what type of bacterial sequences do you have? Is it shotgun or amplicon sequencing?

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Hello, Soxs genes of E coli.

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Hello @gjahanmir

I was chatting with Chloe about this. I'm a little confused about your goals here. Can you tell us more?

This sounds cool! :petri_dish:

Because you are working with bacterial isolates, it should be easy to do genomic sequencing and then assemble these into genomes with either shotgun or long-read sequencing. Or both!

Soxs genes

How did you pick out this gene? Is there a paper you can share with us?

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This is data from our lab (I am given) and I am sorry I dont have any paper to share.

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I understand. I have also been given many old data sets and ask to help process them.

Do you know why they chose the E. coli Soxs genes to amplify and sequence?

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Dear @colinbrislawn,

Thanks for your time. Now it is clear that they only need a simple blast search and allignment to compare all together.

Thanks and Best Regards,

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