Assembly contigs into scaffolds with AMOS

Question

[ben.blais]

Hello, I have a little problem. Indeed, I would like to assemble contigs into scaffolds. I have Two files containing contigs of interest (in fasta format) obtained after de novo assembly and I would like to do a scaffolding.

I wanted to use the AMOScmp tool based on a reference to the .fasta format, but I can't use this tool on the command line. I would like to know if it is possible to get help.

My goal is to assemble contigs in two files into scaffolds to map reads using the result of this step as a reference.

Hoping to have been clear enough, thank you in advance and wish you a great day

[ben.blais]

Hi, thanks you for your help, i will go see it.

Answer 1

[h.mon]

AMOS doesn't seem to be an appropriate tool for what you want to do. The purpose of AMOScmp is to assemble reads using a closely related genome as reference.

It seems you want to perform what is usually called an assembly reconciliation or assembly merging. There are several tools for that, an internet search should help you find some. I haven't done an assembly reconciliation yet, but a recent review doesn't seem encouraging about its usefulness:

A comparative evaluation of genome assembly reconciliation tools