How to concatenate scaffolds in a plant mitochondrial genome assembly

Question

[avaivanov.bg]

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!

[zxzhongxiao]

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!

[ATpoint]

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.

Answer 1

[lagartija]

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;