Hi everyone,
I've sequenced (Illumina; Nextera; 2x250) different strains of Salmonella (size of the genome around 5Mb) and I want to compare the genomes to check if there are related or not: some came from animals the others from patients.
I've cleaned my sequences with trimmomatic before doing the assembly (I used megahit, although now I know it's not the best one) . After that I tried difference analysis:
-REALPHY (contigs and reference genome as input files) to obtain the phylogenetic tree.
-bwa to do the mapping between my contigs and the reference, but I didn't know how to get a single sequence. I checked it with QUAST.
-With mauve I got my contigs ordered according to my reference but not a consensus sequence for each sample and I could not interpret the results very well.
I am quite new in Bioinformatics, so I'd appreciate some advice.
1/If I use two different assemblers (Velvet and Spades), how can I merge both?
2/Is is better in this case to do assembly de novo or just mapping with a reference (I have a high coverage)?
3/One I have the contigs, which software should I used to obtain scaffols? And to obtain a unique sequence I can use in further analysis?
4/Which software would you recommend me for phylogeny? And for clustering? Do you think this would be the best way to answer my problem?
I'd really appreciate any suggestion.
Thank you very much!
Andrea
hi ma'am,
use this site: https://www.patricbrc.org/
it is very easy to analyze genome using this
feel free to ask.further if you have any questions.
Hi Mendem,
Thank you very much for the interesting link!
Do you think I need to annotate my genomes to answer my question or making a phylogeny and analysis of variations will be enough?
Regards,
Andrea
Thank you very much Mathew, it's been really helpful.
I have some doubts about the QUAST report, do you think the number of missaligments in this sample attached is too high?
I'm trying to analysis SNPs variants. I've done call variant with GATK following this pipeline: https://approachedinthelimit.wordpress.com/2015/10/09/variant-calling-with-gatk/ but now a do not know which is the best way to study the homology among samples. Could you recommend me something?
Thank you vey much.
Regards,
Andrea
These are single colony picks... I compared MEGAHit, velvet and spades and in all of them I have several misaligments... (attached). I think I should try with VelvetOptimiser to find the optimal kmer lenght maybe?
The result from FastaAlternateReferenceMaker is the reference FASTA with all the SNPs in my sample or should be intervals?
Once I have my fasta files, which is the best option for the tree?
I tried to do the tree with SNPhylo. It takes the vcf files directly and perform all steps to get the tree, but tells me the files are not big enough to do the analysis. Any other option to do it directly from vcf files or is it better to convert to fasta before?
I found this paper (http://www.genetics.org/content/172/2/743) (attached) in which the author develop a typing method based on SNPs. How can I take this information into consideration when doing the tree?
Thank you very much for your helpful advice!
Andrea
Thank you very much for all the advices Mat. They have been really useful!!!
Best regards,
Andrea
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