Pandora's Toolbox

[samanta]

Hello,

I am developing a toolbox with collection of source codes of efficient bioinformatics programs.
They are available under the condition that you cite the individual authors and not Pandora's toolbox.

My goal is to develop additional code so that we can mix and match them to solve various problems efficiently.

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github page -

https://github.com/homologus/Pandoras-Toolbox/

Blog posts -

Introducing ‘Pandora’s Toolbox’ and ‘Pandora’s Modules’

http://www.homolog.us/blogs/blog/2015/01/05/introducing-pandoras-toolbox-and-pandoras-modules/

An Update on Pandora’s Toolbox

http://www.homolog.us/blogs/blog/2015/01/08/an-update-on-pandoras-toolbox/

The following programs are currently included in the collection.

1. KMC2

2. bwa (included BWAMEM)

3. DALIGNER

4. HMMER3

5. bcalm – de Bruijn graph compressor

6. Minia – assembler

7. samtools – NGS data handling

8. SOAPdenovo2 – genome assembler

9. SOAPdenovo-trans – transcriptome assembler

10. SPAdes – genome assembler

11. Trinity – transcriptome assembler

12. sailfish – RNAseq expression analysis

13. RAPSearch2

14. Tophat

15. Cufflinks

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I would appreciate any thoughts and suggestions.

[GenoMax]

BBMap suite - "Leatherman" tool for NGS data. So many tools that only Brian remembers what is in there and how to use them

FastQC

Subread/featureCounts

Trimmomatic

Qualimap (pretty BAM stats)

STAR

[samanta]

Thanks Genomax.

Trimmomatic is part of Trinity, but I am thinking about moving it in a separate directory. I will look into the rest, but is STAR an unusual aligners after BWA? Do I need to keep multiple aligners?

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I also started a thread here and got some feedback.

https://www.biostars.org/p/126050/

[GenoMax]

Choice is good (and sometimes required) since one aligner may work better (because of the resources available for the end-user) than other. STAR is a good RNA-seq aligner (though it has high memory requirements).

I had not looked at your blog post closely yesterday but after reading the thread on biostars things are more clear. Though I like the docker idea I think that just adds one more layer for a "not-so-computer-savvy" person to deal with. Being able to reliably compile (or better yet having pre-compiled statically linked binaries available, as Heng suggested in biostars post) would make this effort valuable.

[jpummil]

BBMap suite - "Leatherman" tool for NGS data. So many tools that only Brian remembers what is in there and how to use them

FastQC

Subread/featureCounts

Trimmomatic

Qualimap (pretty BAM stats)

STAR

Second these, especially FastQC and BBMap. The "worst" thing about BBMap is that it is perpetually being improved to be more and more robust, so frequent updates need to be installed to be current! Kudo's to Brian!

I'd also throw in Quast for a post-assembly quality assessment tool (though BBMap has one as well).