Fig. 1

Overview of the Falco framework pipelines. a Alignment-only pipeline. The pipeline is composed of the splitting and pre-processing steps from the original Falco framework and the new Spark-based alignment step from the Falco framework. The alignment step is composed of two stages - an alignment stage, where read chunks are aligned and stored in a temporary location in HDFS, and a concatenation stage, where alignment chunks from the same sample are concatenated to obtain the full alignment result. b Transcript-assembly pipeline. The pipeline is also composed of the splitting and pre-processing steps from the original Falco framework in addition to the new Spark-based transcript assembly step from the Falco framework. The transcript assembly step is composed of a number of stages, including an alignment stage, which performs alignment of read chunks and binning of the alignment result; an assembly stage which perform transcript assembly in parallel, and a merging step, where assembled transcripts are merged with the reference annotation to produce an updated annotation