Hello everyone
I'm working on the genome processing of a fish species based on Next Generation Sequencing method. There's not been previous reports of this species sequence and now I have also raw data in Fastq and Fasta formats.
Now, how can I assemble these data?
And also, I've assembled them in Galaxy website through " Create assemblies with Unicycler " path, Is it true? And is the result of such assembling reliable?
Hi Mohsen,
To perform a de novo assembly of the sequence reads you obviously need some assembly software. I assume your lab does not have commercial assembly software such as CLC Genomics workbench?
There are several free assembly programs which you can use to perform a de novo assembly of your reads. I would recommend SPADES (http://cab.spbu.ru/software/spades/) or IDBA-UD as these have been shown in several articles to outperform others as well as not being computer resource hungry (need lots of RAM and runs for very long). Please stay away from Velvet as assembly software. One of the problems with using these programs is that if the user is not experienced with using a command line interface, it makes it difficult to get into. My advice is, that if you are going to stay and work in the biological sciences, that you familiarize yourself with the linux environment as soon as possible as many programs are written just for this operating system. As daunting as it may be, most of the software available comes with a manual and worked examples to show you how to perform the assembly using your files. Another option is joining the mailing list for the particular piece of software you end up using and asking others on the list how to go about installing and running it. You can also e-mail the software creators and ask their help.
Having personally used SPADES and compared it with CLC Genomics workbench I can highly recommend it. If you have a desktop computer available with a spare hard drive (easiest) i would suggest installing linux (Ubuntu 18.10) on it and then SPADES (I use WUBI to install Ubuntu on spare hard drives from Windows desktop). Alternatively you could install VirtualBox on your Windows machine and install an instance of Ubuntu which will let you run SPADES on your machine without too much hassle. Youtube is your friend when it comes to figuring all this stuff out. Look through the SPADES manual to see the use cases they provide and just use your files to do the assembly.
The software will have some variables that you can change to try and improve your assembly, but the default values are usually a good place to start.
My answer is rather generic as i don't give you the exact steps to perform to do the assembly, but hopefully i've mentioned enough things that you could try on your own to get you going.
Regards
Lonnie
Hi Mohsen, I suggest compare the results obtained by Unicycler to those by other sequence assembly program such as EGassembler (www.genome.jp/tools/egassembler/), DNA Baser, or CodonCode Aligner (/www.codoncode.com/).
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