search

mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references
Other
146 stars 27 forks source link

Why is my scaffolded genome larger than the total contig length and my target genome? #49

Closed CristianRiccio closed 5 years ago

CristianRiccio commented 5 years ago

Hi, I have run Ragout with default parameters between a set of contigs (file size 92 M), and a chromosome-length reference genome (99 M) and obtained a gap-free genome of 101 M. How is that possible? I thought Ragout would just order the contigs based on the reference and put Ns in the gaps. Cheers.

mikolmogorov commented 5 years ago

It is possible because Ragout inserts gaps (sequence of Ns) between the scaffolded contigs. It outputs the number of inserted Ns into the log file + you can check .links and / or .agp files to see where the gaps are.