title: Systematic evaluation of spliced alignment programs for RNA-seq data.
abstract: High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction. We observed concordant results on real and simulated RNA-seq data, confirming the relevance of the metrics employed. Future developments in RNA-seq alignment methods would benefit from improved placement of multimapped reads, balanced utilization of existing gene annotation and a reduced false discovery rate for splice junctions.
authors.affiliation: 1] European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK. [2].
authors.forename: Pär G
authors.initials: PG
authors.lastname: Engström
authors.forename: Tamara
authors.initials: T
authors.lastname: Steijger
authors.forename: Botond
authors.initials: B
authors.lastname: Sipos
authors.forename: Gregory R
authors.initials: GR
authors.lastname: Grant
authors.forename: André
authors.initials: A
authors.lastname: Kahles
authors.forename: Gunnar
authors.initials: G
authors.lastname: Rätsch
authors.forename: Nick
authors.initials: N
authors.lastname: Goldman
authors.forename: Tim J
authors.initials: TJ
authors.lastname: Hubbard
authors.forename: Jennifer
authors.initials: J
authors.lastname: Harrow
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigó
authors.forename: Paul
authors.initials: P
authors.lastname: Bertone
mesh_terms: D000818:Animals; D002874:Chromosome Mapping / Q000379:methods; D019295:Computational Biology / Q000379:methods; D005091:Exons; D005189:False Positive Reactions; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D020014:K562 Cells; D051379:Mice; D012326:RNA Splicing; D012333:RNA, Messenger / Q000378:metabolism; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012333:RNA, Messenger