I am putting together an e-book to describe the tools in Pandora’s Toolbox for Bioinformatics. It is free. So, feel ‘free’ to grab a copy !! Beware - the current version is very far from complete, but once you get a copy, you will be able to access the improved versions at no extra cost.
Pandora’s Toolbox includes a small subset of mostly recent bioinformatics programs (BLAST, HMMER, RAPsearch2, BWAMEM, Samtools, KMC2, BCALM, Minia, SPAdes, SOAPdenovo, SOAPdenovo-trans, Trinity, Sailfish, Tophat, Cufflink, DALIGNER, HGAP, DBG2OLC, PHYLIP) to help a researcher solve problems in biology. One overarching goal is to let them get a feel for the algorithms and not use the programs as black-boxes. Therefore, each chapter describes a program and includes the following sections - (i) history, (ii) how to run, (iii) features, (iv) details of algorithm, (v) details of code, (vi) further readings.
Status of the genome assembly book
I had been working extensively on the genome assembly book, but decided to take a detour from it to put together this manual. That is because I seemed to be referring to the software programs in Pandora’s Toolbox again and again in the genome assembly book and felt that it would help to get the topic covered well elsewhere. I plan to spend a week to complete and edit the sections in this ‘Pandora’s Toolbox for Bioinformatics’ manual and then go back to the assembly book right after that.
Readers, please help
I picked a wide and representative subset of programs in Pandora’s Toolbox for Bioinformatics. Each of the program is reasonably efficient and algorithmically innovative as well. However, if you think any important category or program is not covered, please let me know.