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?
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.
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.
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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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.
It is fungal genome. When I run SPAdes, it aborts in the middle. I assume SPAdes is not perfect for this.
What is your RAM availability and dataset size?