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Can we assembly the draft sequences that is assembled by another genome assembler

If I have already assembled the genome sequences with a lot of contigs and short readings, can I use another software to further assembly the one that was assembled? I used abyss to do the 1st round, but I have a lot of short readings. If I use SPAdes to continue to assembly ... will it do any better?

assembly genome sequencing next-gen
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written by flavobacteria • flavobacteria

You could look at scaffolding software. But as @shenwei said below directly using original data with SPAdes is the best option for bacterial genome assemblies.

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written by GenoMax GenoMax

It is fungal genome. When I run SPAdes, it aborts in the middle. I assume SPAdes is not perfect for this.

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written by flavobacteria • flavobacteria

What is your RAM availability and dataset size?

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written by Joe Joe

3 answers

Directly using SPAdes.

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written by shenwei356 shenwei356

I used scaffolding softwares like sspace several times for bacterial genome, but the results were not ideal. So I just assembled with SPAdes.

If you have reference complete genomes, reference-assisted assembly using Ragout is also an option. If not, you can also filter the spades contigs based on coverage and length. Bandage is also an assistant tool to check assembly graph and filter contigs.

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written by shenwei356 shenwei356

Alternative is to provide SPAdes with so-called trusted contigs of your ABySS assembly.

It sometimes can be beneficial to combine assemblies from different assembly strategies. If you have multiple sequencing rounds/technologies and de novo assemblies you could also try to merge those assemblies using contig assemblers (i.e. MIRA could do that) or merger tools like quickmerge.

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written by ALchEmiXt ALchEmiXt

Can anyone help with this command spades.py --trusted-contigs mtla90-contigs.fa o all It gives error messages: == Error == you should specify at least one unpaired, paired-end, or high-quality mate-pairs library!

I used the --trusted-contigs, why it still asks for one unpaired, paired-end, or high-quality mate-pairs library

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written by flavobacteria • flavobacteria

You need to provide a trusted contigs file along with the rest of the data you want to use to assemble.

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written by GenoMax GenoMax

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