How to determine inverted repeat borders in chloroplast genome?

01 January 1970 0 5K Report

Hello,

I am facing an issue in determining Inverted repeat borders of chloroplast genome?

I have done Illumina sequencing of tree genome. The chloroplast genome was assembled using Novoplasty assembler. After assembling, I received an average of five expected assemblies for each different kmer. All the assemblies were varied in length between 50-2000bp. Later, I had checked the gene orientation with the closely placed reference genome. But the borders of inverted repeats are varied in all assemblies.

May I know, what is the best way to recognize the correct borders of inverted repeats in the chloroplast genome?

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