Ballgown bridges the gap between transcriptome assembly and expression analysis

Abstract

243 16. Janin, L., Rosone, G. & Cox, A.J. Bioinformatics 30, 24–30 (2014). 17. DePristo, M.A. et al. Nat. Genet. 43, 491–498 (2011). 18. Yu, Y.W., Yorukoglu, D. & Berger, B. in Research in Computational Molecular Biology: 18th Annual International Conference, RECOMB 2014—Proceedings (ed. Sharan, R.) 385–399 (Springer, 2014). 19. Kelley, D.R., Schatz, M.C. & Salzberg, S.L. Genome Biol. 11, R116 (2010). 20. Grabherr, M.G. et al. Nat. Biotechnol. 29, 644–652 (2011). 21. Cánovas, R., Moffat, A. & Turpin, A. Bioinformatics 30, 2130–2136 (2014). 22. Li, H. et al. Bioinformatics 25, 2078–2079 (2009). 23. Li, H. & Durbin, R. Bioinformatics 26, 589–595 (2010). 24. Langmead, B. & Salzberg, S.L. Nat. Methods 9, 357– 359 (2012). steps, such as variant calling (e.g., using SAMTools or GATK), can be carried out in the usual way. Our optimized and parallelized implementation of Quartz is available, along with a high-quality human genome k-mer dictionary (Supplementary Software). We also provide here preliminary results on how Quartz changes compression levels and variant-calling accuracy on an Escherichia coli genome, indicating Quartz’s utility beyond human genomics (Supplementary Fig. 12). With improvements in sequencing technologies increasing the pace at which genomic data is generated, quality scores will require ever greater amounts of storage space; compressive quality scores will become crucial to fully realizing the potential of large-scale genomics. Our data here, in contrast to previous results21, indicate that the twin goals of compression and accuracy do not have to be at odds with each other. Although total compression comes at the cost of accuracy (Supplementary Fig. 6), and quality score recalibration generally decreases compressibility (Supplementary Table 1), there is a happy medium at which we can get good compression and improved accuracy. The Quartz software (available at http://quartz. csail.mit.edu and in Supplementary Software) will greatly benefit any researchers who are generating, storing, mapping or analyzing large amounts of DNA, RNA, CHIP-seq or exome sequencing data.