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How to find out the specific strain in NGS data?

I have a whole genome sample from a phage/bacteria (little is known about the sample). I did the assembly with CLC genomics workbench and did a BLASTn for the scaffolds where I am getting hits from many organisms along with hits from a particular bacteriophage of interest (i know the phage speices but not the specific strain).

Now from the blast results, there are several hits for several strains of that phage. How can I be sure about the strain?

phage blast bacteriophage
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written by lakhujanivijay lakhujanivijay

Strain level identification is a tough nut to crack unless you have reference genomes available for all strains. You may want to increase stringency of your BLAST (e.g. disallow gaps, mismatches) if you want to narrow down the list of possibilities.

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written by GenoMax GenoMax

2 answers

See these papers:

http://nar.oxfordjournals.org/content/early/2014/02/12/nar.gku138.full

Strain/species identification in metagenomes using genome-specific markers

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3630013/

Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3934542/

COV2HTML: A Visualization and Analysis Tool of Bacterial Next Generation Sequencing (NGS) Data for Postgenomics Life Scientists

http://www.nature.com.sci-hub.cc/nrmicro/journal/v10/n9/full/nrmicro2853.html#

Going viral: next-generation sequencing applied to phage populations in the human gut

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written by natasha.sernova natasha.sernova

I ended up using PHASTER for prophage identification. Here is the link for paper:

http://nar.oxfordjournals.org/content/early/2016/05/03/nar.gkw387.abstract

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written by lakhujanivijay lakhujanivijay

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