I am using Velvet_1.2.10 assembler to obtain de novo sequence of an amplicon. I have obtained contigs given by velvetg containing 10 nodes and n50 value of 1023. How do I know the order and orientation of the contigs and assemble them to obtain the original sequence?
You could use a contig scaffolder in order to reorder the contigs based on a set of reference genomes. I'd give MeDuSa a try. Maybe this is exactly what you are looking for:
web: http://combo.dbe.unifi.it/medusa/
local: https://github.com/combogenomics/medusa
One way is to scaffold the contigs, overview here, a bit of an error-prone process
Alternatively, you could order the contigs against a known reference, with tools like ABACAS. If you follow the pagit protocol you could try to close the gaps between the contigs.
But importantly, in the end, you HAVE to check for errors, with tools like REAPR... I hope that helps
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r42
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