Question: How to concatenate scaffolds in a plant mitochondrial genome assembly
0
gravatar for avaivanov.bg
6 months ago by
avaivanov.bg0 wrote:

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!

ADD COMMENTlink modified 6 months ago by lagartija10 • written 6 months ago by avaivanov.bg0
1
gravatar for lagartija
6 months ago by
lagartija10
lagartija10 wrote:

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;

ADD COMMENTlink written 6 months ago by lagartija10
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