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Old 08-05-2013, 08:20 AM   #1
NGS group
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Question How to call the core genome of bacteria

Hi everyone,

I am trying to build a SNP tree from a set of bacterial genomes (the same species), and the first step is going to get the core genome. However, I did not find any detail workflow for that. Does anyone know some software or pipelines that can complete such task?

Thank you very much!

Victor
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Old 08-05-2013, 11:09 AM   #2
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You could look around NCBI's ftp. Maybe your species is already in the SNP DB? If not, you might have to do all-vs-all blasts and clustering (maybe OrthoMCL) to find out the shared genes. What you want might be possible with eutils too. Oh and there's this pipeline called HAL that might do what you want..

Last edited by rhinoceros; 08-05-2013 at 11:17 AM.
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Old 08-05-2013, 12:39 PM   #3
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How many genomes are you working with? And are you working with assemblies or raw reads?

For a smaller number of genome assemblies, you could do whole genome alignments with Mugsy (http://sourceforge.net/projects/mugsy/files/) or ProgressiveMauve (http://gel.ahabs.wisc.edu/mauve/), filter for blocks that are common to all genomes, then infer a phylogeny from the concatenated alignment? Is that what you had in mind?

Jason
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Old 08-05-2013, 02:01 PM   #4
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Hi rhinoceros,

Thank you for your reply. The aim of my project is to distinguish outbreak strains, so I have to do the analysis by myself. The HAL pipeline is what I want exactly. However I am not so familiar with commend line, is there any other more user-freindly pipeline or programs under Windows system?

Victor
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Originally Posted by rhinoceros View Post
You could look around NCBI's ftp. Maybe your species is already in the SNP DB? If not, you might have to do all-vs-all blasts and clustering (maybe OrthoMCL) to find out the shared genes. What you want might be possible with eutils too. Oh and there's this pipeline called HAL that might do what you want..
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Old 08-05-2013, 02:11 PM   #5
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Hi Jason,

Thank you for your reply. I am working with 15-20 genomes, which have been assembled. I am using Mauve now, but I think it is not easy to filter the common sequences by manual in Mauve. Do you mean that I just concatenate all common sequences by copy paste? Which alignment and phylogenetic tools are you going to use afterwards? Also Mauve?

Victor

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Originally Posted by themerlin View Post
How many genomes are you working with? And are you working with assemblies or raw reads?

For a smaller number of genome assemblies, you could do whole genome alignments with Mugsy (http://sourceforge.net/projects/mugsy/files/) or ProgressiveMauve (http://gel.ahabs.wisc.edu/mauve/), filter for blocks that are common to all genomes, then infer a phylogeny from the concatenated alignment? Is that what you had in mind?

Jason
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Old 08-06-2013, 08:39 AM   #6
themerlin
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Victor,

If you have an aversion to command line tools, you could try this web server:

http://cge.cbs.dtu.dk/services/snpTree/

You can upload assemblies, fastqs, vcfs, and/or bams and it will compute a tree. I haven't used it, but it might fit your needs.

Jason
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Old 08-06-2013, 09:13 AM   #7
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This is a nice web tool. Thank you very much, Jason.

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Victor,

If you have an aversion to command line tools, you could try this web server:

http://cge.cbs.dtu.dk/services/snpTree/

You can upload assemblies, fastqs, vcfs, and/or bams and it will compute a tree. I haven't used it, but it might fit your needs.

Jason
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