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30. Leinonen R, Sugawara H, Shumway M. International nucleotide sequence database C. The
sequence read archive. Nucleic Acids Res. 2011;39(Database issue):D19–21.
31. Armstrong J, Fiddes IT, Diekhans M, Paten B. Whole-genome alignment and comparative
annotation. Annu Rev Anim Biosci. 2019;7:41–64.
32. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, et al. A survey
of best practices for RNA-seq data analysis. Genome Biol. 2016;17:13.
33. Lee RS, Behr MA. Does choice matter? Reference-based alignment for molecular epidemiology
of tuberculosis. J Clin Microbiol. 2016;54(7):1891–5.
34. Sherman RM, Salzberg SL. Pan-genomics in the human genome era. Nat Rev Genet. 2020;21
(4):243–54.
35. Engstrom PG, Steijger T, Sipos B, Grant GR, Kahles A, Ratsch G, et al. Systematic evaluation
of spliced alignment programs for RNA-seq data. Nat Methods. 2013;10(12):1185–91.
36. Trapnell C, Salzberg SL. How to map billions of short reads onto genomes. Nat Biotechnol.
2009;27(5):455–7.
37. Baruzzo G, Hayer KE, Kim EJ, Di Camillo B, FitzGerald GA, Grant GR. Simulation-based
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38. Bushnell B, editor. BBMap: a fast, accurate, splice-aware aligner. Berkeley: Lawrence Berkeley
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39. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal
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40. Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and
EST sequences. Bioinformatics. 2005;21(9):1859–75.
41. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment
of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol.
2013;14(4):R36.
42. Benjamin AM, Nichols M, Burke TW, Ginsburg GS, Lucas JE. Comparing reference-based
RNA-Seq mapping methods for non-human primate data. BMC Genomics. 2014;15:570.
43. Zakeri M, Srivastava A, Almodaresi F, Patro R. Improved data-driven likelihood factorizations
for transcript abundance estimation. Bioinformatics. 2017;33(14):i142–i51.
44. Wu DC, Yao J, Ho KS, Lambowitz AM, Wilke CO. Limitations of alignment-free tools in total
RNA-seq quantification. BMC Genomics. 2018;19(1):510.
45. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9
(4):357–9.
46. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using
mapping quality scores. Genome Res. 2008;18(11):1851–8.
47. Frankish A, Diekhans M, Ferreira A-M, Johnson R, Jungreis I, Loveland J, et al. GENCODE
reference annotation for the human and mouse genomes. Nucleic Acids Res. 2018;47(D1):
D766–D73.
48. Schaarschmidt S, Fischer A, Zuther E, Hincha DK. Evaluation of seven different RNA-Seq
alignment tools based on experimental data from the model plant Arabidopsis thaliana. Int J Mol
Sci. 2020;21(5):1720.
49. Holzer M, Marz M. De novo transcriptome assembly: a comprehensive cross-species comparison of short-read RNA-Seq assemblers. Gigascience. 2019;8(5):giz039.
172
R. Bharti and D. G. Grimm
sequencing data. Bioinformatics. 2011;27(1):130–1.
28. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads.
EMBnet J. 2011;17(1):3.
29. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data.
Bioinformatics. 2014;30(15):2114–20.
30. Leinonen R, Sugawara H, Shumway M. International nucleotide sequence database C. The
sequence read archive. Nucleic Acids Res. 2011;39(Database issue):D19–21.
31. Armstrong J, Fiddes IT, Diekhans M, Paten B. Whole-genome alignment and comparative
annotation. Annu Rev Anim Biosci. 2019;7:41–64.
32. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, et al. A survey
of best practices for RNA-seq data analysis. Genome Biol. 2016;17:13.
33. Lee RS, Behr MA. Does choice matter? Reference-based alignment for molecular epidemiology
of tuberculosis. J Clin Microbiol. 2016;54(7):1891–5.
34. Sherman RM, Salzberg SL. Pan-genomics in the human genome era. Nat Rev Genet. 2020;21
(4):243–54.
35. Engstrom PG, Steijger T, Sipos B, Grant GR, Kahles A, Ratsch G, et al. Systematic evaluation
of spliced alignment programs for RNA-seq data. Nat Methods. 2013;10(12):1185–91.
36. Trapnell C, Salzberg SL. How to map billions of short reads onto genomes. Nat Biotechnol.
2009;27(5):455–7.
37. Baruzzo G, Hayer KE, Kim EJ, Di Camillo B, FitzGerald GA, Grant GR. Simulation-based
comprehensive benchmarking of RNA-seq aligners. Nat Methods. 2017;14(2):135–9.
38. Bushnell B, editor. BBMap: a fast, accurate, splice-aware aligner. Berkeley: Lawrence Berkeley
National Lab.(LBNL); 2014.
39. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal
RNA-seq aligner. Bioinformatics. 2012;29(1):15–21.
40. Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and
EST sequences. Bioinformatics. 2005;21(9):1859–75.
41. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment
of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol.
2013;14(4):R36.
42. Benjamin AM, Nichols M, Burke TW, Ginsburg GS, Lucas JE. Comparing reference-based
RNA-Seq mapping methods for non-human primate data. BMC Genomics. 2014;15:570.
43. Zakeri M, Srivastava A, Almodaresi F, Patro R. Improved data-driven likelihood factorizations
for transcript abundance estimation. Bioinformatics. 2017;33(14):i142–i51.
44. Wu DC, Yao J, Ho KS, Lambowitz AM, Wilke CO. Limitations of alignment-free tools in total
RNA-seq quantification. BMC Genomics. 2018;19(1):510.
45. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9
(4):357–9.
46. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using
mapping quality scores. Genome Res. 2008;18(11):1851–8.
47. Frankish A, Diekhans M, Ferreira A-M, Johnson R, Jungreis I, Loveland J, et al. GENCODE
reference annotation for the human and mouse genomes. Nucleic Acids Res. 2018;47(D1):
D766–D73.
48. Schaarschmidt S, Fischer A, Zuther E, Hincha DK. Evaluation of seven different RNA-Seq
alignment tools based on experimental data from the model plant Arabidopsis thaliana. Int J Mol
Sci. 2020;21(5):1720.
49. Holzer M, Marz M. De novo transcriptome assembly: a comprehensive cross-species comparison of short-read RNA-Seq assemblers. Gigascience. 2019;8(5):giz039.
172
R. Bharti and D. G. Grimm