What are OBITools4? #

The development of OBITools began at LECA ( University of Grenoble) in the early 2000s, at the same time as the development of DNA metabarcoding methods in the same laboratory. The idea behind the OBITools project was to provide a set of UNIX command-line tools that mimic standard UNIX shell commands such as grep, uniq or wc, but which work on DNA sequence files. Unlike standard UNIX tools, where the processing unit is a line of text, with OBITools the processing unit is a sequence record. In addition, some commands implementing algorithms specific to the processing of DNA metabarcoding data have been added, making OBITools one of the sequence processing tools widely used on UNIX-like systems, suitable for the analysis of DNA metabarcoding data.

OBITools were originally developed in Python version 2, with some computationally intensive code written in C. They were adapted to the volumes of DNA metabarcoding data generated by 454 pyrosequencing in the early 2000s. With the advent of Solexa and Illumina sequencers, data sizes increased considerably, making OBITools less efficient. Coupled with the switch to Python version 3, OBITools became difficult to implement.

OBITools4 are the latest version of OBITools . Unlike OBITools3, OBITools4 follow the same philosophy as OBITools1 and OBITools2. OBITools4 are a complete rewrite of the OBITools code in GO, an efficient compiled programming language. This language also enables code to be parallelized to take advantage of the multi-core architectures of today’s computers.

The most important thing to understand about OBITools is that it is not a pipeline for processing DNA metabarcoding data. OBITools are a set of tools that allow you to easily build your own pipeline for processing your DNA metabarcoding data according to your biological questions.