I observe two extremely different phenotypes in my bacterial population. There are about 30 isolates for each phenotype. All of these isolates are whole-genome sequenced. Now I want to look for the unique SNPs that are present in only one phenotype. Are there any web-based tool or program I can use to do that? I am very new to bioinformatics. Thank you!
If your sequenced data is in the form of short raw reads from Next generation platforms, they are needed first to be subjected for quality filtering, and adapter trimming. Various tools are available for this purpose like fastQC and fastp etc. The quality filtered reads are then mapped onto the reference genome to create an alignment. This is done with sequence alignment tools e.g. BWA. Duplicates are removed/masked using specific tools e.g., Picard. Once you have created the alignment now it’s time for variant calling (SNPs, and InDel calling). Various pipelines are available there for variant calling, e.g., Genome Analysis Toolkit (GATK), and DeepVariant from Google. Once SNPs have been identified, the final step is now to annotate and predict the effects of the variants. Variant annotation is done using specific tools e.g., SnpEff, GEMINI, and ANNOVAR. You can also use the web-based platform for all of these analyses e.g., Galaxy (https://usegalaxy.org/).
Best Wishes!
Sawar
parSNP and GNGR
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0524-x
https://harvest.readthedocs.io/en/latest/content/parsnp.html
You just put your FASTA files in the comand line and then the output file is a tree with an alignment of your SNPS.
good luck
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