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Fig. 5 | BMC Bioinformatics

Fig. 5

From: K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity

Fig. 5

Stratification of the runtime in terms of individual steps within both versions of Inchworm, for the experimental mouse dataset (see Table 1). OI represents Original Inchworm; MR represents MapReduce-Inchworm. On the X-axis, original represents the original version of Inchworm, while 32–192 represent the numbers of compute nodes allocated for MapReduce-Inchworm. The original Inchworm is divided into three steps: step1 corresponds to Jellyfish [44]; step 2 corresponds to parsing kmers; and step3 corresponds to Inchworm contig construction. MapReduce-Inchworm is divided into six steps: an initial step for splitting input reads and steps 1–5. The initial step splits an input file (containing the RNA-Seq reads) into multiple files according to the number of allocated compute nodes. Steps 1 to 5 of the main algorithm are described in detail in Methods. Results are given with pagesize assigned to 2GB, cf. Fig. 3(b)

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