Which Are The Best Collections Of Bioinformatics Tools For Ngs Analysis And Sequence Files Management?

Question

[Geparada]

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!

[Medhat]

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

Answer 1

[brentp]

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.:

   • UCSC and MySQL server

   • Ensembl

   • 1000 genomes

[Geparada]

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!!

Answer 2

[Gww]

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.

[Boboppie]

Galaxy is definitely worth trying.

[Geparada]

I agree. Currently we're using galaxy.

Answer 3

[Drio]

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.

[Geparada]

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!

Answer 4

[Malcolm.Cook]

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

[Hranjeev]

Cool and quite comprehensive!

Answer 5

[Martin A Hansen]

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

[Mat]

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).