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How to concatenate scaffolds in a plant mitochondrial genome assembly

Dear All,

I have an Illumina PE data (2X 2,3GB, reads of 150bp) and I am trying to assemble a mitochondrial genome of ~500 Kb expected size. I used ABySS for contig generation and SSPACE for scaffolding. Finally, I got 65 scaffolds and i used MAUVE to order them against a reference genome.

My question is : How to concatenate scaffolds in order to obtain the complete genome sequence? Do I need to look for overlapping between them or just to merge scaffolds into a single fasta file ?

I tried CAP3 and BLAST for overlapping, but i did't find any overlaps.

Thank you in advance!

assembly mitochondrial genome
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updated by zxzhongxiao • zxzhongxiao • written by avaivanov.bg • avaivanov.bg

Hi, you must have solved the problem? Can you share your experience here? Thats would be very helpful!

Recently, I am trying assembling a plant mitochondrial genome. To date, I already got ~17 'mito' contigs, ~650kb and hope to merge them further if possible!

Cheers!

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written by zxzhongxiao • zxzhongxiao

Please open a new question, describing in depth what you've done so far and what the problems are. The OP of this question has not been logged in in a year, you won't get an answer from them.

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written by ATpoint ATpoint

1 answer

Seams difficult if you don't have overlapping sequences. Maybe you could try scaffolding your assemblage with your PE library with NpScarf to see if it's more complete than with SSPACE;

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written by lagartija lagartija

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