Question: genome assembly software
gravatar for nora
4.4 years ago by
nora40 wrote:

hello can anyone suggest me a free software for genome assembly but must be donne on a Windows 10 or 7 thank you in advance

assembly genome • 4.6k views
ADD COMMENTlink modified 2.5 years ago by MetaTK20 • written 4.4 years ago by nora40

Free and Windows-only together, are deal breakers.

What is the expected size of the genome? How big is your dataset?

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by GenoMax96k

the probleme is not in the genome size , most softwares that I found require MacOS or Linux system, and I tried with cap3 in the windows system but I have not succeeded

ADD REPLYlink written 4.4 years ago by nora40

The genome size is part of the problem and influences the answer. Not all software is appropriate for all genome sizes.

ADD REPLYlink written 4.4 years ago by igor12k

You'll be best off running a virtual machine with linux in it on your Windows computer. Then you can use the normal bioinformatics programs.

ADD REPLYlink written 4.4 years ago by Devon Ryan98k

ok , thank you very much

ADD REPLYlink written 4.4 years ago by nora40

If you change "Windows" to "web-based", you will have more possible answers and you will still be able to run it on Windows.

ADD REPLYlink written 4.4 years ago by igor12k
gravatar for Lesley Sitter
4.4 years ago by
Lesley Sitter550
Lesley Sitter550 wrote:

Keep in mind that most of the people here (bioinformaticians) are Linux based, and there is a good reason we stick to Linux for this type of stuff (windows based software are often unstable when dealing with this type of data sets).... BUT!

DNA Star It's not my favorite because in my opinion it's unstable when dealing with large genomes or a large set of libraries, but it's windows based and allows free trials giving you 2 weeks of free use, and are often available through universities for discounted prices

Geneious Again, trial license is possible and discount for students.

Other than that VMware with Ubuntu and bioinformatics software like @Devon Ryan mentioned is a good option (it's how I play with data on my personal laptop) or you can make a dual boot installation of linux

Another method is getting someone to set up a system called Galaxy, which is essentially an interface for Linux software... it gives windows users a clear GUI with which they can do stuff like assemblies, annotations, etc, problem is that it has to be set up by someone on a Linux backend

And I haven't used this, but there is also a bioinformatics Linux OS called Biolinux Apparently it's a ready to boot USB OS, so you just plug it in, get your PC to start from USB and you have a complete bioinformatics toolkit at your finger tips :D

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Lesley Sitter550

DNASTAR It's not my favorite because it's highly unstable.

This must to be your personal experience. My institution has been using DNASTAR for about a year and I have never heard from anyone that it is highly unstable. OP had asked for "free" software and DNASTAR and Geneious do not make the cut on that account. It was the reason CLC Workbench was not mentioned. CLC happens to have a reasonably good assembly program, but it is not free.

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by GenoMax96k
gravatar for MetaTK
2.5 years ago by
MetaTK20 wrote:

You could use the DocMind Analyst but its also not free. However, I want to mention it because its great for beginners and those who don't want to deal with Linux. It has a graphical user interface and you can choose between different assemblers (SPAdes, Skesa, A5) and different assembly options.

It offers a pipeline that includes read trimming (Trimmomatic), assembly, postprocessing (Pilon) and assembly statistics. There are also other pipelines like core genome phylogeny analysis with SNP/Indel calling and so on. You can start it in Windows and just choose a server in the AWS cloud. They also have good tutorials on their website. Its focused on bacterial genome or metagenomics analysis at the moment.

ADD COMMENTlink written 2.5 years ago by MetaTK20

You added not free disclaimer but if you are affiliated with this product/company then you should include that in the post. If you are only a fan of the software then that is ok too.

BTW: There appears to be NO information about pricing structure on the product on the website.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by GenoMax96k

DocMind Analyst is free. Fees apply for AWS infrastructure.

ADD REPLYlink written 2.3 years ago by DMA20
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