Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis

BMC Bioinformatics

Table 2 Running time (seconds) and memory usage (gigabytes) by Yanagi to generate segment library for fruit fly (BDGP6) and human (GRCh38) genomes, for both the preprocessing and segmentation steps

	BDGP6		GRCh38
	time(s)	memory(GB)	time(s)	memory(GB)
Preprocessing	13	0.9	112	1.5
Segmentation
L=40	20	0.4	248	1.3
L=108	20	0.4	250	1.3
L=1000	20	0.4	228	1.3
L=10000	8.5	0.4	77	1.3
Rapmap Indexing (4 Threads)
L=108	103	0.8	420	2.6
Txs	121	1.1	480	3.7
Rapmap Quantification (8 Threads)
L=108	236	0.7	220	2.1
Txs	292	1.2	416	3.1

Time for the preprocessing step does not include the time to load the FASTA and GTF files. Most of the memory usage is from loading the input data in both steps. Running on a 6-core 2.1 GHz AMD processor, using single-threaded processes. The lower half shows the time and memory usage for running Rapmap’s quasi-mapping using the segments library and the the full transcriptome, to quantify samples of 40M paired-end reads, each of length 101bp.

ISSN: 1471-2105