Genome assembly tools

Question

[glady]

I have prokaryotic dataset, sequenced by Amplicon Sequencing. Can some one help me in downloading and using MIRA. And even if you can suggest me some other good assembly tools like MIRA, well be really helpfull.

[GenoMax]

Before we get a list of all known assemblers in answers below please modify this post to include what kind of genome you are working with (pro-, eukaryotic) along with what kind of data you have (genomic, RNAseq, illumina, pacbio etc). If the genome size/ploidy is known that would be useful to know as well.

This would help narrow the suggestions down to a list you can use right away.

[Benn]

MIRA can be found here: https://sourceforge.net/projects/mira-assembler/

I don't know what kind of data you have, but the manual is pretty complete I would say...

Answer 1

[Xin]

I am not familiar with MIRA. I use Trinity for De-novo assembly (Initial assembly). After that, I use Cap3 to remove redundant sequences and build a meta-assembly. I think these two tools are good.

Answer 2

[harold.smith.tarheel]

Spades and Ray are two commonly used tools for genome assembly.

[WouterDeCoster]

From his initial question it's not clear whether OP is referring to genome or transcriptome assembly tools...

[harold.smith.tarheel]

The question is entitled "genome assembly tools" - that's clear enough for me :-).

[WouterDeCoster]

Right :p I see that the question has also been modified, adding a bit of information.

[GenoMax]

Well .. Yes and no. I don't know of a genome sequencing method that uses amplicon sequencing. Am I missing something? So it sounds like OP wants to assemble amplicons (and not a genome)?

[WouterDeCoster]

That's why I went with 'a bit of information', considering we now know it's prokaryotic. That's an improvement on getting to an answer I would say. A small step forwards. It looks definitely like a strange approach to use amplicons. We also have no idea about read lengths, genome size, repeat lengths,...

Next time you want to assemble a small genome, get yourself a MinION sequencer :-D