Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco

BMC Genomics

Table 1 Runtime comparison for alignment of single cell datasets with and without the Falco framework

System	Nodes	Mouse - embryonic stem cell (hours)		Human - brain (hours)
		STAR	HISAT2	STAR	HISAT2
Standalone	1 (1 process)	34.9	42.7	11.1	9.8
	1 (12 processes)	20.2	14.9	5.2	3.1
	1 (16 processes)	N/A	14.9	N/A	3.0
Falco	10	8.0	5.9	1.7	1.2
	20	4.7	3.6	1.0	0.8
	30	3.8	2.9	0.8	0.6
	40	3.5	2.6	0.7	0.6

Standalone number of processes indicates the number of FASTQ file pairs that are processed in parallel. Timing for Falco includes initialisation and configuration time which are approximately 10 min. Runtime for STAR with 16 processes is not available as some STAR processes are killed by the operating system, resulting in failure of the job

ISSN: 1471-2164