Fig 1.
Flowchart of NGS-QCbox pipeline illustrating the two modes of usage namely quick and complete.
NGS-QCbox comprises of two workflow modes namely quick and complete. In quick mode, read/base level metrics are computed in parallel using Raspberry, an in-house tool, both before and after quality trimming. On the other hand, complete mode is full-fledged quality control and variant calling pipeline that integrates quick mode and additionally generates genome coverage information in parallel. Quality of the data generated could be assessed using this information.
Fig 2.
The menu driven interface for NGS-QCbox for quick and complete mode respectively.
(a) Shows the prompt and the parameters such as cut-off phred score, minimum read length after trimming, data source and number of processors to be used for the quick QC mode. (b) Complete QC mode adds more parameters to quick mode like information related to the genome (bowtie index, genome size, number of processors used by bowtie).
Table 1.
A comparative account of the features of NGS-QCbox pipeline with five similar pipeline/tools.
Table 2.
Parallel performance comparison of NGS-QCbox with other tools/pipelines.