- Girke, Thomas (2014) systemPipeR: NGS workflow and report generation environment. NA, NA: NA; URL
- Howard, Brian E, Hu, Qiwen, Babaoglu, Ahmet Can, Chandra, Manan, Borghi, Monica, Tan, Xiaoping, He, Luyan, Winter-Sederoff, Heike, Gassmann, Walter, Veronese, Paola, Heber, Steffen (2013) High-throughput RNA sequencing of pseudomonas-infected Arabidopsis reveals hidden transcriptome complexity and novel splice variants. PLoS One, 8: e74183; URL
- Kim, Daehwan, Pertea, Geo, Trapnell, Cole, Pimentel, Harold, Kelley, Ryan, Salzberg, Steven L (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14: R36; URL
- Langmead, Ben, Salzberg, Steven L (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9: 357–359; URL
- Lawrence, Michael, Huber, Wolfgang, Pag`{e}s, Herv'{e}, Aboyoun, Patrick, Carlson, Marc, Gentleman, Robert, Morgan, Martin T, Carey, Vincent J (2013) Software for computing and annotating genomic ranges. PLoS Comput. Biol., 9: e1003118; URL
- Liao, Yang, Smyth, Gordon K, Shi, Wei (2013) The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res., 41: e108; URL
- Li, H, Durbin, R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25: 1754–1760; URL
- Li, Heng (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv [q-bio.GN], NA: NA; URL
- Wu, T D, Nacu, S (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics, 26: 873–881; URL