ARNApipe: A balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments

Bioinformatics

Volumn 33, Issue 11, 2017, Pages 1727-1729

  Alonso, Arnald ^a,b   Lasseigne, Brittany N ^a   Williams, Kelly ^a   Nielsen, Josh ^a   Ramaker, Ryne C ^a,c   Hardigan, Andrew A ^a,c   Johnston, Bobbi ^a   Roberts, Brian S ^a   Cooper, Sara J ^a   Marsal, Sara ^b   Myers, Richard M ^a  

^a HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

^b HOSPITAL UNIVERSITARI VALL D HEBRON   (Spain)

^c UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ALTERNATIVE RNA SPLICING; COMPUTER ANALYSIS; GENOTYPING TECHNIQUE; HUMAN; METABOLISM; PROCEDURES; SEQUENCE ANALYSIS; SOFTWARE; WORKFLOW;

ALTERNATIVE SPLICING; COMPUTING METHODOLOGIES; GENOTYPING TECHNIQUES; HUMANS; RNA; SEQUENCE ANALYSIS, RNA; SOFTWARE; WORKFLOW;

EID: 85021334511     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btx023     Document Type: Article

References (6)

1. Conesa, A. et al. (2016) A survey of best practices for RNA-seq data analysis. Genome Biol., 17, 19.
2. Finotello, F., and Di Camillo, B. (2015) Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis. Brief. Funct. Genom., 14, 130-142.
3. Koboldt, D.C. et al. (2012) VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res., 22, 568-576.
4. Maher, C.A. et al. (2009) Transcriptome sequencing to detect gene fusions in cancer. Nature, 458, 97-101.
5. McGettigan, P.A. (2013) Transcriptomics in the RNA-seq era. Curr. Opin. Chem. Biol., 17, 4-11.
6. Scholz, M.B. et al. (2012) Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr. Opin. Biotechnol., 23, 9-15.