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:
user does not need to install all the software on its local server;
results generated by different containers can be organized in pipelines;
reproducible research is guarantee by the possibility of sharing the docker images used for the analysis.
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.
At the present time all functions requiring some sort of calculation are embedded in the following docker images:
docker.io/repbioinfo/demultiplexing.2017.01 used by demultiplexing
docker.io/repbioinfo/annotate.2017.01 used by rnaseqCounts, rsemanno
docker.io/repbioinfo/bwa.2017.01 used by bwaIndexUcsc, bwa
docker.io/repbioinfo/chipseq.2017.01 used by chipseqCounts, chipseq
docker.io/repbioinfo/r332.2017.01 used by experimentPower, sampleSize, wrapperDeseq2
docker.io/repbioinfo/mirnaseq.2017.01 used by mirnaCounts
docker.io/repbioinfo/rsemstar.2017.01 used by rnaseqCounts, rsemstarIndex, rsemstarUscsIndex
docker.io/repbioinfo/skewer.2017.01 used by skewer, rnaseqCounts
docker.io/repbioinfo/xenome.2017.01 used by xemone, xenomeIndex
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.
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.
At the present time are available the following workflows: