Correction: L-RNA-scaffolder: Scaffolding genomes with transcripts (BMC Genomics (2013) 14 (604) DOI: 10.1186/1471-2164-14-604);L_RNA_scaffolder: Scaffolding genomes with transcripts

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Xue, Wei ^a,b,c   Li, Jiong Tang ^a   Zhu, Ya Ping ^a,b   Hou, Guang Yuan ^a   Kong, Xiang Fei ^a,b   Kuang, You Yi ^a   Sun, Xiao Wen ^a  

^a SOUTH CHINA SEA FISHERIES RESEARCH INSTITUTE   (China)

^b SHANGHAI OCEAN UNIVERSITY   (China)

^c Chinese Academy of Sciences   (China)

Author keywords

Genome; L_RNA_scaffolder; Scaffolding; Transcriptome

Indexed keywords

MOLECULAR SCAFFOLD; TRANSCRIPTOME;

ACCURACY; ARTICLE; COMPUTER PROGRAM; GENE SEQUENCE; GENETIC MODEL; GENETIC POLYMORPHISM; GENETIC PROCEDURES; GENOME; HIGH THROUGHPUT SCREENING; HUMAN GENOME; MOLECULAR LIBRARY; RNA TRANSCRIPTION; ZEBRA FISH;

DANIO RERIO; PINCTADA;

ANIMALS; GENOME, HUMAN; GENOMICS; HUMANS; PINCTADA; RNA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSCRIPTOME; ZEBRAFISH;

EID: 84883798077     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-019-5856-1     Document Type: Erratum

References (32)

1. Williams LJ, Tabbaa DG, Li N, Berlin AM, Shea TP, Maccallum I, Lawrence MS, Drier Y, Getz G, Young SK, et al. Paired-end sequencing of Fosmid libraries by Illumina. Genome Res 2012, 22(11):2241-2249. 10.1101/gr.138925.112, 3483553, 22800726.
2. Peng Z, Zhao Z, Nath N, Froula JL, Clum A, Zhang T, Cheng JF, Copeland AC, Pennacchio LA, Chen F. Generation of long insert pairs using a Cre-LoxP Inverse PCR approach. PLoS One 2012, 7(1):e29437. 10.1371/journal.pone.0029437, 3253782, 22253722.
3. Geng C, Chen Y, Wu K, Cai Q, Wang Y, Lang Y, Cao H, Yang H, Wang J, , et al. Asan Paired-end sequencing of long-range DNA fragments for de novo assembly of large, complex Mammalian genomes by direct intra-molecule ligation. PLoS One 2012, 7(9):e46211. 10.1371/journal.pone.0046211, 3459883, 23029438, Asan.
4. Kent WJ, Haussler D. Assembly of the working draft of the human genome with GigAssembler. Genome Res 2001, 11(9):1541-1548. 10.1101/gr.183201, 311095, 11544197.
5. Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, et al. The reality of pervasive transcription. PLoS Biol 2011, 9(7):e1000625. discussion e1001102, 10.1371/journal.pbio.1000625, 3134446, 21765801.
6. Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature 2013, 496(7446):498-503. 10.1038/nature12111, 23594743.
7. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, et al. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res 2012, 22(3):557-567. 10.1101/gr.131383.111, 3290791, 22147368.
8. Parra G, Bradnam K, Ning Z, Keane T, Korf I. Assessing the gene space in draft genomes. Nucleic Acids Res 2009, 37(1):289-297. 10.1093/nar/gkn916, 2615622, 19042974.
9. Takeuchi T, Kawashima T, Koyanagi R, Gyoja F, Tanaka M, Ikuta T, Shoguchi E, Fujiwara M, Shinzato C, Hisata K, et al. Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology. DNA Res 2012, 19(2):117-130. 10.1093/dnares/dss005, 3325083, 22315334.
10. Salamov AA, Solovyev VV. Ab initio gene finding in Drosophila genomic DNA. Genome Res 2000, 10(4):516-522. 10.1101/gr.10.4.516, 310882, 10779491.
11. Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, Yang P, Zhang L, Wang X, Qi H, et al. The oyster genome reveals stress adaptation and complexity of shell formation. Nature 2012, 490(7418):49-54. 10.1038/nature11413, 22992520.
12. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010, 20(2):265-272. 10.1101/gr.097261.109, 2813482, 20019144.
13. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res 2009, 19(6):1117-1123. 10.1101/gr.089532.108, 2694472, 19251739.
14. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 2011, 27(4):578-579. 10.1093/bioinformatics/btq683, 21149342.
15. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, et al. Ensembl 2011. Nucleic Acids Res 2011, 39:D800-806. 10.1093/nar/gkq1064, 3013672, 21045057.
16. Li H, Wang J, Mor G, Sklar J. A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells. Science 2008, 321(5894):1357-1361. 10.1126/science.1156725, 18772439.
17. Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM. Transcriptome sequencing to detect gene fusions in cancer. Nature 2009, 458(7234):97-101. 10.1038/nature07638, 2725402, 19136943.
18. Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R, Lazarevic D, Hayashizaki Y, Carninci P. The complexity of the mammalian transcriptome. J Physiol 2006, 575(Pt 2):321-332. 1819450, 16857706.
19. Yang L, Duff MO, Graveley BR, Carmichael GG, Chen LL. Genomewide characterization of non-polyadenylated RNAs. Genome Biol 2011, 12(2):R16. 10.1186/gb-2011-12-2-r16, 3188798, 21324177.
20. Junemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, et al. Updating benchtop sequencing performance comparison. Nat Biotechnol 2013, 31(4):294-296. 10.1038/nbt.2522, 23563421.
21. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29(7):644-652. 10.1038/nbt.1883, 3571712, 21572440.
22. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013, 10(6):563-569. 10.1038/nmeth.2474, 23644548.
23. Au KF, Underwood JG, Lee L, Wong WH. Improving PacBio long read accuracy by short read alignment. PLoS One 2012, 7(10):e46679. 10.1371/journal.pone.0046679, 3464235, 23056399.
24. Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR, et al. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res 2012, 40:D918-923. 10.1093/nar/gkr1055, 3245018, 22086951.
25. Seqclean http://compbio.dfci.harvard.edu/tgi/software.
26. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002, 12(4):656-664. 187518, 11932250.
27. Replicating web-based Blat percent identity and score calculations http://genome.ucsc.edu/FAQ/FAQblat.html#blat4.
28. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012, 1(1):18. 10.1186/2047-217X-1-18, 3626529, 23587118.
29. Gao S, Sung WK, Nagarajan N. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. J Comput Biol 2011, 18(11):1681-1691. 10.1089/cmb.2011.0170, 3216105, 21929371.
30. Salmela L, Makinen V, Valimaki N, Ylinen J, Ukkonen E. Fast scaffolding with small independent mixed integer programs. Bioinformatics 2011, 27(23):3259-3265. 10.1093/bioinformatics/btr562, 3223363, 21998153.
31. Dayarian A, Michael TP, Sengupta AM. SOPRA: Scaffolding algorithm for paired reads via statistical optimization. BMC Bioinforma 2010, 11:345.
32. Cox MP, Peterson DA, Biggs PJ. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinforma 2010, 11:485.