Measuring sequence similarity between draft genomes
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4.1 years ago
Raghul ▴ 200

Hi

I have 2 draft genomes of closely related bacterial species. I have downloaded the data from NCBI Genome. Their sequencing methods & assembly tool differs. I want to compare these 2 whole genomes & measure the sequence similarity. What are the tools available to do that? I am using windows OS! My first objective is to find how much similar are they, for eg. say 80% or 90% ?

some Details for species 1 Assembly type: na Assembly level: Scaffold Genome representation: full RefSeq assembly and GenBank assembly identical: yes WGS Project

some Details for species 2 Assembly type: na Assembly level: Scaffold Genome representation: full RefSeq assembly and GenBank assembly identical: yes WGS Project Assembly method: Unicycler v. 0.4.7 Expected final version: no Genome coverage: 81.4x Sequencing technology: Illumina HiSeq

Total sequence length 3,827,202 & 3,804,728 (species 1 & 2) Total ungapped length 3,826,102 & 3,789,834

Hope the newly added info above helps, Thank you for all your replies!

Thanx
Raghul

genome_comparison draft_genome sequence_similarity • 1.1k views
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Thanx

Please use professional language on professional/scientific forums, not IM/SMS jargon.

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Mensur's suggestions below are a good start. Appropriate methods will somewhat depend on how close you expect the sequences to be.

Are these 2 sequences of different isolates of the same bacteria? Assemblies of the exact same clone? Are they entirely different species?

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4.1 years ago
Mensur Dlakic ★ 27k

FastANI and pyani will do alignment-free comparisons of whole genomes.

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4.1 years ago
h.mon 35k

Are the two draft genome different assemblies of the same data set, e.g., using different assemblers, or different sequencing reads filtering? Or are they closely related, but different strains? Please provide more information.

You can use QUAST to access the quality of genome assemblies and compare several assemblies. You can also use Mauve to align the assemblies and visualize the alignment.

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