Processing of shotgun metagenome data

Question

[kocharovskayaj]

Hello, I have a whole metagenome shotgun data processed by trimmomatic, metaspades and bowtie. Please tell me what to do next? It is necessary to find out what organisms are in the samples, as well as to search for genes. Thank you for your answer.

[scarlettpigany]

Hello, I'm working on a similar topic, and I would be grateful if you could share the steps and the tools you used. If you have a Git repository with your pipeline, please don't hesitate to share it with me. Thank you!

Answer 1

[Carambakaracho]

some suggestions you could go with

• Classification with Kraken2
• Annotation with Prodigal
• Binning using metabat2 (or concoct)
• Assess completeness with BUSCO.

Then you could head down the rabbit hole of functional annotation transfer to figure out what your microbiome is capable of (the MicrobeAnnotator published in Jan 2021 looks promising).

[scarlettpigany]

Hello, I'm a bioinformatics student, and I would greatly appreciate it if you could share the entire pipeline with me. By that, I mean the steps, why we apply them, and the tools involved. Thank you in advance, and I hope you can help answer my question.

[Carambakaracho]

Hi scarlettpigany, I've moved into a different position since then - I wouldn't be able to describe anything more up to date than what I wrote above. May I suggest you ask a more detailed question on the front page. Make sure to include some rough details of what you want to do, what your starting point is (for example raw reads -> assembly -> binning -> classification -> annotation -> completeness). Best, C.