This visualization requires the use of local alignment of scafftigs (scaffold broken by a stretch of Ns/unfilled scaffold gaps). Thus, if repetitive regions exist they may not align properly even if correctly scaffolded especially if surrounded by these scaffold gaps.
This visualization requires the use of local alignment of scafftigs (scaffold broken by a stretch of Ns/unfilled scaffold gaps). Thus, if repetitive regions exist they may not align properly even if correctly scaffolded especially if surrounded by these scaffold gaps.