Contents

0.1 Introduction

SeqBox was developed to facilitate the use of computing demanding applications in the field of NGS data analysis.

SeqBox uses docker containers that embed demanding computing tasks (e.g. short reads mapping) into isolated containers.

This approach provides multiple advantages:

SeqBox comes with the R engine, docker4seq, its graphical interface, 4SeqGUI, and all dockers images installed in the NUC6I7KYK, Intel mini-computer equipped with 32GB GB RAM and 250GB/500GB Internal SSD.

0.2 Dockers containers

At the present time all functions requiring some sort of calculation are embedded in the following docker images:

0.2.1 docker container nomenclature

In case of updates required to solve bugs, which do not affect the calculation docker.io/rcaloger/XXXXX.YYYY.ZZ the fiels ZZ will be updated.

In case of updates which affect the calculation, e.g. new release of Bioconductor libraries, the field YYYY will be updated. Previous versions will be maintained to guarantee the reproducibility of any previous analisys.

0.2.2 Reproducibility

The file containers.txt, which indicates the Docker images available in the local release of docker4seq is saved within any folder generated with docker4seq functions.

0.3 Available workflows

At the present time are available the following workflows: