Benchmarked Software

Name Pubmed Version
CLC Genomics Workbench CLC Genomics Workbench website 8.5
ContextMap 2 ContextMap 2: fast and accurate context-based RNA-seq mapping (Bonfert 2015) 2.6.0
CRAC CRAC: an integrated approach to the analysis of RNA-seq reads (Philippe 2013) 2.4.0
GSNAP Fast and SNP-tolerant detection of complex variants and splicing in short reads (Wu 2010) 2015-9-29
HISAT HISAT: a fast spliced aligner with low memory requirements. (Kim 2015) 0.1.6beta
HISAT2 HISAT: a fast spliced aligner with low memory requirements. (Kim 2015) 2.0.0beta
MapSplice MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery (Wang 2010) 2.2.0
NovoAlign Novocraft Technologies website 3.02.13
OLego OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds (Wu 2013) 1.1.6
RUM Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM) (Grant 2011) 2.0.5_06
SOAPSplice SOAPsplice: genome-wide ab initio detection of splice junctions from RNA-Seq data (Huang 2011) 1.10
STAR STAR: ultrafast universal RNA-seq aligner (Dobin 2013) 2.5.0a
Subread The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote (Liao 2013) 1.5.0
TopHat2 TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions (Kim 2013) 2.1.0

Other tools used in this project

Name Pubmed Version
Bowtie Ultrafast and memory-efficient alignment of short DNA sequences to the human genome (Langmead 2009) 1.1.2
Bowtie 2 Fast gapped-read alignment with Bowtie 2 (Langmead 2012) 2.2.5
BWA Fast and accurate short read alignment with Burrows-Wheeler transform (Li 2009) 0.7.12
Cutadapt Cutadapt Removes Adapter Sequences From High-Throughput Sequencing Reads (Martin 2011) 1.10
SAMtools The Sequence Alignment/Map format and SAMtools (Li 2009) 0.1.19
USeq Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks (Nix 2008) 8.9.5

Our Code to run and evaluate the presented algorithms

Scripts that run the benchmarked software can be found at bitbucket/baruz. (You can also download the scripts here.)
To compare the results of each algorithm to the truth please refer to this repository github/khayer. (You can also download the scripts here.)