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Potential chimeric contig persists after RaGOO

See original GitHub issue

Hi Michael,

I’ve used RaGOO to scaffold my PacBio contigs against a Sanger reference genome. Here is my command:

ragoo.py -b -g 100 -i 0.6 -C "$ASMN" "$REFN"

Here is the alignment between the reference I used (y-axis) and the resulting RaGOO scaffolds (x-axis).

s160_2_edited_to_ragoo paf plot

Everything looks correct except for the highlighted region at the end of chromosome E. Below is a zoom of that region:

I am confused as to why do I still see a difference between the arrangement of my scaffolds and the reference I used.
I understand that my assembly has some extra sequence that is not present in the reference, but I don’t understand why that inverted segment on the right side is not placed in the correct spot and orientation.

Let me know if you have any tips to help me understand this.

Issue Analytics

State:
Created 4 years ago
Comments:8 (5 by maintainers)

Top GitHub Comments

1reaction

malongecommented, Dec 17, 2019

I believe that it would break at the left breakpoint in your example.

1reaction

malongecommented, Dec 15, 2019

Hi there,

Just one of them needs to be met.

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