News: Free draft copy of book on bioinformatics tools
gravatar for ugly.betty77
3.1 years ago by
United States
ugly.betty771.0k wrote:

Hello all,

I am putting together an ebook to describe a number of useful bioinformatics tools. The book is under development, and V0.1 is freely available at the following link.

[In fact, if you grab V0.1, all updates will also be freely available to you based on leanpub rules.]

Here is what I am trying to achieve. I work with a number of biologists and they often complain about - (i) not knowing what bioinformatics tools to use for their large data files, (ii) the tools they have need more RAM etc. than what they have and (iii) not knowing how to mix/match multiple tools to do something efficiently and (iv)  interpreting the results coming from various programs. For example, does Trinity giving 350,000 assembled transcripts mean the organism has 350K genes?

So, I am building together a minimal set of efficient programs to help them so that I do not need to go over the same explanation many times. The project is moving slowly, but I am making progress.

Here are some of the relevant posts -

Pandora's Toolbox - a collection of bioinformatics programs

All thoughts and suggestions are welcome.


ADD COMMENTlink modified 3.1 years ago by h.mon15k • written 3.1 years ago by ugly.betty771.0k

Great job! I like the idea of having a pre-made solutions  for using bioinformatics utilities. But often times, with each revision of these programs/utilities, options keep changing and your book will soon become outdated. How are going to deal with that?


ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by arnstrm1.6k


The book can be updated any time and readers can download the new version for free. So, changing options is not a problem (except it takes my time). 

Moreover, the idea is to give newcomers some place to start from, not give a total package describing everything in a program. I am not trying to replace the well-maintained documentation sites by the authors of the programs.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by ugly.betty771.0k
gravatar for h.mon
3.1 years ago by
h.mon15k wrote:

Great initiative, and thanks for sharing. Some thoughts/suggestions:

1. a protein / gene / mRNA / EST mapper - Spaln, GMAP, ...

2. a genome viewer - IGV, IGB, Tablet, ...

3. variant calling will be covered using samtools mpileup?

4. PHYLIP is great, but all other tools are geared towards big NGS data, PHYLIP would be a bottleneck (it has been some time since I used it, but I think it would not handle a phylogenomic-sized dataset)


ADD COMMENTlink written 3.1 years ago by h.mon15k

Thank you for the great suggestions !! I agree about your comment on PHYLIP, and decided to keep it as a placeholder until finding enough time to check other options and find something better. Do you have any suggestion?

ADD REPLYlink written 3.1 years ago by ugly.betty771.0k

RAxML, ExaML and ExaBayes, all from the Exelixis lab, are being used for phylogenomics. There are others, but these are the ones I have familiarity.

ADD REPLYlink written 3.1 years ago by h.mon15k
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