Post Genome Assembly
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You can have a try with "Contiguator" or "CAR"
There doesn't seem to be a publication available for this software yet, but I've found Medusa to be very useful:
https://github.com/combogenomics/medusa
It seems like many of the other scaffolding tools require paired-end reads or are designed for prokaryote genomes.
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kcamnairb •
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You have what type reads to scaffold? Some people have do evaluation of assembly scaffolding tools (https://rmcsoftwareinc.files.wordpress.com/2015/02/hunt_scaffolding_tools.pdf)
@Orange
I have single end reads from Ion torrent and my aim is to remove gaps from the scaffolds and also to check whether number of contigs are decreasing or not but for this I can use reference only to check whether the alignment is correct or not other than this I cant use reference for filling gaps and all.
Any suggestion will be a great help
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