Which Are The Best Collections Of Bioinformatics Tools For Ngs Analysis And Sequence Files Management?
5
2
Entering edit mode
11.5 years ago
Geparada ★ 1.5k

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-sequencing • 16k views
ADD COMMENT
0
Entering edit mode
ADD REPLY
11
Entering edit mode
11.5 years ago
brentp 24k

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 COMMENT
0
Entering edit mode

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 REPLY
6
Entering edit mode
11.5 years ago
Gww ★ 2.7k

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 COMMENT
0
Entering edit mode

Galaxy is definitely worth trying.

ADD REPLY
0
Entering edit mode

I agree. Currently we're using galaxy.

ADD REPLY
3
Entering edit mode
11.5 years ago
Drio ▴ 920

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 COMMENT
0
Entering edit mode

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 REPLY
3
Entering edit mode
11.5 years ago
Malcolm.Cook ★ 1.3k

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

ADD COMMENT
0
Entering edit mode

Cool and quite comprehensive!

ADD REPLY
1
Entering edit mode
11.5 years ago

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 COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 2613 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6