Question: Can we assembly the draft sequences that is assembled by another genome assembler
1
gravatar for flavobacteria
2.2 years ago by
United States
flavobacteria40 wrote:

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?

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by flavobacteria40

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.

ADD REPLYlink written 2.2 years ago by genomax67k

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

ADD REPLYlink written 2.2 years ago by flavobacteria40

What is your RAM availability and dataset size?

ADD REPLYlink written 2.2 years ago by jrj.healey12k
1
gravatar for shenwei356
2.2 years ago by
shenwei3564.6k
China
shenwei3564.6k wrote:

Directly using SPAdes.

ADD COMMENTlink written 2.2 years ago by shenwei3564.6k

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.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by shenwei3564.6k
1
gravatar for ALchEmiXt
2.2 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

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.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by ALchEmiXt1.9k
0
gravatar for flavobacteria
2.2 years ago by
United States
flavobacteria40 wrote:

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

ADD COMMENTlink written 2.2 years ago by flavobacteria40

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

ADD REPLYlink written 2.2 years ago by genomax67k
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