windows bioinformatics programs

Question

[grigoryangeorg]

Hello everyone! I wanted to ask if anyone could suggest programs for windows with the ability to analyze the data of NGS sequencing (sorry in advance for possible errors, I'm just not English-speaking, I write through a translator). I will be grateful to those who help.

[grigoryangeorg]

I will definitely try the options that you suggested to me. thank you so much

Answer 1

[GenoMax]

There are no free programs that will work on Windows that can analyze NGS data*. There are commercial applications that can though. CLC Genomics Workbench, Geneious are a couple of examples. There are others (DNASTAR, Partek Genomics suite) that can do some NGS analysis as long as the data has been aligned elsewhere.

You may be best off using Galaxy if you have no command line experience as one free option.

** - There may be some that are feature limited but for a request like this requester is more than likely looking for something more feature complete.

[JC]

UGENE has some tools and runs on windows. Also take a look into WLS2.

But, if you are doing analysis, better to do in Linux

[swbarnes2]

Even if Windows tools exist, if you want help, there is a much bigger community of people who can help with unix tools than can help with Windows tools, the major exception I think being galaxy. (Though note that this board isn't an IT help line or a unix command line tutorial)

[grigoryangeorg]

you know, I tried to do it through CLC Genomics Workbench, but I didn’t quite figure out how to do it could you explain to me if it’s not difficult for you?

Answer 2

[ATpoint]

First of all don't worry about your english, most of us are non-native speakers, your text is perfectly fine.

As genomax indicates freeware on Windows and bioinformatics is a difficult combination. I strongly encourage you to switch to a Unix system, e.g. on your machine in a dual-boot or VM-fashion. Most tools and software is Unix-based plus the Unix command line is powerful for data manipulation, you are going to need it.

[grigoryangeorg]

thanks for the advice I would have done so, but my personal computer is quite old and unviable, so I'm afraid to conduct any manipulations with it

Answer 3

[shelkmike]

I recommend UGENE. It is a free and versatile program.

[grigoryangeorg]

I tried to do through it, however it freezes when analyzing NGS. then on the official site I read that Linux is needed for this function

Answer 4

[dariober]

I don't know if this qualifies as a viable option for you - cygwin is a Linux emulator for windows. Since most bioinformatics programs are open source you should be able to install and run them on cygwin/windows. Maybe bioconda package will also run fine under cygwin? That would solve a lot of complications related to the installations. cygwin would be a more lightweight solution than a dual boot Linux/Windows but it would have also the disadvantages of a not-really-linux system.

[russhh]

Although I agree with Dario, I've had more success running bioinformatics tools on the Windows subsystem for Linux, WSL, compared with cygwin: https://docs.microsoft.com/en-us/windows/wsl/install-win10

[grigoryangeorg]

thank you very much, I will try

Answer 5

[Randy H]

https://wgsextract.github.io/ is on Win10, Linux and MacOS. A new, much more powerful release due out soon. Based on Samtools, bcftools, bwa, etc.

Also see the document http://bit.ly/38jnxnK written to get mostly Win10 users up and running with tools. Most variants revolve around WSL or VirtualBox installs. But also simply using the WGSExtract Win10 binaries delivered today.

Buried in both the above is http://bit.ly/2FSSjH6 which describes a quick way to get just the binaries on Win10.

Wish BioConda would provide WIn10 releases along with their Linux and MacOS ones. Then WGS Extract could switch over to a Conda app in a heartbeat and avoid many, many issues. It took me < 30 mins to install CygWin64 and then htslib.org sources compiled to that. Longest time is manually getting all the packages needed to compile as CygWin64 does not have a command-line / scripted package manager (you have to manually search and select dozens of packages; and not super packages but the binaries separate from the additional needed link libraries!). Somebody needs to get an apt-get equivalent working for them. Know WIn10 is a dead horse for many. But most non-bioinformatic users around seem to still be stuck with it. (I have been on Unix since 1976 and so have no issues there ...)