Question: Which Are The Best Collections Of Bioinformatics Tools For Ngs Analysis And Sequence Files Management?
2
gravatar for Geparada
7.5 years ago by
Geparada1.3k
Cambridge
Geparada1.3k wrote:

Hi! Currently I've realised that there are available many public scripts to manage NGS data and sequence files in general.

Last month, I installed some packages for UCSC genome source tools from Bergman Lab and tools like pslTobed, saved a lot of time to me!

Now we are analysing NGS data, and I wonder if you know some collections of bioinformatics tools which can help me (like biopieces).

Thanks!!!

next-gen open tool sequencing • 13k views
ADD COMMENTlink modified 7.5 years ago by Drio910 • written 7.5 years ago by Geparada1.3k

http://toolkit.tuebingen.mpg.de/

ADD REPLYlink written 2.6 years ago by Medhat8.0k
11
gravatar for brentp
7.5 years ago by
brentp22k
Salt Lake City, UT
brentp22k wrote:

I agree with @drio that there is no single tool. So your best bet is to

  1. master a scripting language (or many). Learn the bioinformatics libraries available for that language.

  2. learn linux command-line tools (grep, awk, cut, and others).

  3. learn the most used bioinformatics tools. e.g.:

    • one (or preferably many) short-read aligners

    • samtools

    • an NGS viewer (IGV is a good one to start)

    • Bedtools

    • A means to view and filter your NGS reads

    • and certainly many others depending on your specific focus.

  4. Then start to learn some of the common data repositories. e.g.:

ADD COMMENTlink written 7.5 years ago by brentp22k

I'm not looking for a single tool, I'm looking for collections of tools like samtools and bedtools, that I didn't know before. Thanks!!

ADD REPLYlink written 7.5 years ago by Geparada1.3k
6
gravatar for Gww
7.5 years ago by
Gww2.6k
Canada
Gww2.6k wrote:

I haven't seen it listed yet but bioconductor has a massive collection of different tools for high-throughput analysis. There is also galaxy, which is quite nice. It wraps a lot of the tools already mentioned in other answers.

ADD COMMENTlink written 7.5 years ago by Gww2.6k

Galaxy is definitely worth trying.

ADD REPLYlink written 7.5 years ago by Boboppie520

I agree. Currently we're using galaxy.

ADD REPLYlink written 7.5 years ago by Geparada1.3k
3
gravatar for Drio
7.5 years ago by
Drio910
United States
Drio910 wrote:

There is no one stop tool.

What people does is to rely in a few set of tools (PICARD, samtools, GATK, bwa) and build their own pipelines and scripts on top of that. You add other core tools depending what type of next-gen projects you are working on( re-sequencing, RNA-seq, de-novo assembly, etc ...)

BTW, I wrote a package manager that I use to quickly deploy my toolbox in new machines. If you look at the recipes directory you'll find the names of those tools.

ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by Drio910

I'm asking for these "few set of tools". We started some time ago and we mainly use the tools available on Galaxy. I want to know others set of tools for NGS analysis. Thanks!

ADD REPLYlink written 7.5 years ago by Geparada1.3k
3
gravatar for Malcolm.Cook
7.5 years ago by
Malcolm.Cook900
kansas, usa
Malcolm.Cook900 wrote:

here is a long list: http://seqanswers.com/wiki/Software/list

ADD COMMENTlink written 7.5 years ago by Malcolm.Cook900

Cool and quite comprehensive!

ADD REPLYlink written 7.5 years ago by Hranjeev1.4k
1
gravatar for Martin A Hansen
7.5 years ago by
Martin A Hansen3.0k
Denmark
Martin A Hansen3.0k wrote:

A scripting language will get your job done. However, using tools off the shelf will save heaps of time in the long run. A lot of tool packages exists with all the tools you need for basic sequence analysis. None of these tool packages interact very well - which is a shame. It would be interesting, if they shared a common interface. The one in Biopieces is very simple and straightforward. Here are a few tool packages I remember on top of my head:

  1. Samtools
  2. Bedtools
  3. FastX toolkit
  4. EMBOSS
  5. Biopieces
ADD COMMENTlink written 7.5 years ago by Martin A Hansen3.0k

But note that FastX toolkit was written in a time that read lengths were 39nuc.; it doesn't always deal well with longer reads (e.g. with 105nuc reads clipper does not work accurately).

ADD REPLYlink written 6.8 years ago by Mat40
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