Schulte D, Close TJ, Graner A, Langridge P, Matsumoto T, Muehlbauer G, Sato K, Schulman AH, Waugh R, Wise RP, Stein N. The international barley sequencing consortium--at the threshold of efficient access to the barley genome. Plant Physiol. 2009;149:142–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gill BS, Appels R, Botha-Oberholster AM, Buell CR, Bennetzen JL, Chalhoub B, Chumley F, Dvorak J, Iwanaga M, Keller B, et al. A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics. 2004;168:1087–96.
Article
PubMed
PubMed Central
Google Scholar
Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, et al. A chromosome conformation capture ordered sequence of the barley genome. Nature. 2017;544:427–33.
Article
CAS
PubMed
Google Scholar
The International Wheat Genome Sequencing Consortium (IWGSC): Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science. 2018;361:eaar7191.
Maccaferri M, Harris NS, Twardziok SO, Pasam RK, Gundlach H, Spannagl M, Ormanbekova D, Lux T, Prade VM, Milner SG, et al. Durum wheat genome highlights past domestication signatures and future improvement targets. Nat Genet. 2019;51(5):885–95. https://doi.org/10.1038/s41588-019-0381-3.
Article
CAS
PubMed
Google Scholar
Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, et al. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature. 2017;551:498–502.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ling HQ, Ma B, Shi X, Liu H, Dong L, Sun H, Cao Y, Gao Q, Zheng S, Li Y, et al. Genome sequence of the progenitor of wheat a subgenome Triticum urartu. Nature. 2018;557:424–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H, Hale I, Mascher M, Spannagl M, Wiebe K, et al. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science. 2017;357:93–7.
Article
CAS
PubMed
Google Scholar
McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, et al. A physical map of the human genome. Nature. 2001;409:934–41.
Article
CAS
PubMed
Google Scholar
Beier S, Himmelbach A, Schmutzer T, Felder M, Taudien S, Mayer KF, Platzer M, Stein N, Scholz U, Mascher M. Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes. Plant Biotechnol J. 2016;14:1511–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, et al. Structural and functional partitioning of bread wheat chromosome 3B. Science. 2014;345:1249721.
Article
PubMed
CAS
Google Scholar
Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Muñoz-Amatriaín M, Close TJ, Wise RP, Schulman AH, et al. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J. 2013;76:718–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chapman JA, Mascher M, Buluc A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, et al. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol. 2015;16:26.
Article
PubMed
PubMed Central
Google Scholar
Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol. 2013;31:1119.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kaplan N, Dekker J. High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat Biotechnol. 2013;31:1143.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lam ET, Hastie A, Lin C, Ehrlich D, Das SK, Austin MD, Deshpande P, Cao H, Nagarajan N, Xiao M, Kwok PY. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol. 2012;30:771–6.
Article
CAS
PubMed
Google Scholar
Zhu T, Wang L, Rodriguez JC, Deal KR, Avni R, Distelfeld A, McGuire PE, Dvorak J, Luo MC. Improved genome sequence of wild emmer wheat zavitan with the aid of optical maps. G3 (Bethesda). 2019;9:619–24.
CAS
Google Scholar
Callaway E. Small group scoops international effort to sequence huge wheat genome. Nature News. 2017. https://doi.org/10.1038/nature.2017.22924.
Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, et al. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. Genome Res. 2017;27:885–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marcais G, Yorke JA, Dvorak J, Salzberg SL. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm. Genome Res. 2017;27:787–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zimin AV, Puiu D, Hall R, Kingan S, Clavijo BJ, Salzberg SL. The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum. Gigascience. 2017;6(11):1–7. https://doi.org/10.1093/gigascience/gix097.
Monat C, Schreiber M, Stein N, Mascher M. Prospects of pan-genomics in barley. Theor Appl Genet. 2019;132(3):785–96. https://doi.org/10.1007/s00122-018-3234-z.
Article
PubMed
Google Scholar
Himmelbach A, Walde I, Mascher M, Stein N. Tethered chromosome conformation capture sequencing in Triticeae: a valuable tool for genome assembly. Bio-protocol. 2018;8:e2955.
Article
CAS
PubMed
PubMed Central
Google Scholar
Padmarasu S, Himmelbach A, Mascher M, Stein N. In situ hi-C for plants: an improved method to detect long-range chromatin interactions. Methods Mol Biol. 1933;2019:441–72.
Google Scholar
Bushnell B, Rood J, Singer E. BBMerge - accurate paired shotgun read merging via overlap. PLoS One. 2017;12:e0185056.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li H. BFC: correcting Illumina sequencing errors. Bioinformatics. 2015;31:2885–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chikhi R, Limasset A, Medvedev P. Compacting de Bruijn graphs from sequencing data quickly and in low memory. Bioinformatics. 2016;32:i201–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chikhi R, Rizk G. Space-efficient and exact de Bruijn graph representation based on a bloom filter. Algorithms Mol Biol. 2013;8:22.
Article
PubMed
PubMed Central
CAS
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Journal. 2011;17:10–2.
Article
Google Scholar
O’Connell J, Schulz-Trieglaff O, Carlson E, Hims MM, Gormley NA, Cox AJ. NxTrim: optimized trimming of Illumina mate pair reads. Bioinformatics. 2015;31:2035–7.
Article
PubMed
CAS
Google Scholar
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2012;1:18.
Article
PubMed
PubMed Central
Google Scholar
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;1:7.
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet. 2000;16:276–7.
Article
CAS
PubMed
Google Scholar
Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: a fast and accurate Illumina paired-end reAd mergeR. Bioinformatics. 2014;30:614–20.
Article
CAS
PubMed
Google Scholar
Melsted P, Halldorsson BV. KmerStream: streaming algorithms for k-mer abundance estimation. Bioinformatics. 2014;30:3541–7.
Article
CAS
PubMed
Google Scholar
Mohamadi H, Khan H, Birol I. ntCard: a streaming algorithm for cardinality estimation in genomics data. Bioinformatics. 2017;33:1324–30.
CAS
PubMed
PubMed Central
Google Scholar
Zimin AV, Marcais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics. 2013;29:2669–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L. BESST--efficient scaffolding of large fragmented assemblies. BMC Bioinformatics. 2014;15:281.
Article
PubMed
PubMed Central
Google Scholar
Gao S, Bertrand D, Chia BK, Nagarajan N. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees. Genome Biol. 2016;17:102.
Article
PubMed
PubMed Central
CAS
Google Scholar
Matsumoto T, Tanaka T, Sakai H, Amano N, Kanamori H, Kurita K, Kikuta A, Kamiya K, Yamamoto M, Ikawa H, et al. Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol. 2011;156:20–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Team RC. R: a language and environment for statistical computing, vol. 2017. Vienna: R Foundation for Statistical Computing; 2016.
Google Scholar
Sahlin K, Chikhi R, Arvestad L. Assembly scaffolding with PE-contaminated mate-pair libraries. Bioinformatics. 2016;32:1925–32.
Article
PubMed
Google Scholar
Ghurye J, Pop M, Koren S, Bickhart D, Chin CS. Scaffolding of long read assemblies using long range contact information. BMC Genomics. 2017;18:527.
Article
PubMed
PubMed Central
CAS
Google Scholar
Beier S, Himmelbach A, Colmsee C, Zhang X-Q, Barrero RA, Zhang Q, Li L, Bayer M, Bolser D, Taudien S, et al. Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Scientific Data. 2017;4:170044.
Article
CAS
PubMed
PubMed Central
Google Scholar
Himmelbach A, Ruban A, Walde I, Šimková H, Doležel J, Hastie A, Stein N, Mascher M. Discovery of multi-megabase polymorphic inversions by chromosome conformation capture sequencing in large-genome plant species. Plant J. 2018;96(6):1309–16. https://doi.org/10.1111/tpj.14109.
Article
CAS
PubMed
Google Scholar
Lu F-H, McKenzie N, Kettleborough G, Heavens D, Clark MD, Bevan MW. Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries. GigaScience. 2018;7:giy053.
Article
PubMed Central
CAS
Google Scholar
Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K. TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. Plant Physiol. 2009;150:1135–46.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005;21:1859–75.
Article
CAS
PubMed
Google Scholar
Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007;8:973.
Article
CAS
PubMed
Google Scholar
International Barley Genome Sequencing Consortium. A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012;491:711.
Article
CAS
Google Scholar
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, et al. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009;326:1112–5.
Article
CAS
PubMed
Google Scholar
Putnam NH, O’Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, Troll CJ, Fields A, Hartley PD, Sugnet CW, et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 2016;26:342–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210–2.
Article
CAS
PubMed
Google Scholar
Joyce BL, Haug-Baltzell AK, Hulvey JP, McCarthy F, Devisetty UK, Lyons E. Leveraging CyVerse resources for de novo comparative transcriptomics of underserved (non-model) organisms. J Vis Exp. 2017;(123). https://doi.org/10.3791/55009.
Schmutzer T, Bolger ME, Rudd S, Chen J, Gundlach H, Arend D, Oppermann M, Weise S, Lange M, Spannagl M, et al. Bioinformatics in the plant genomic and phenomic domain: the German contribution to resources, services and perspectives. J Biotechnol. 2017;261:37–45.
Article
CAS
PubMed
Google Scholar
Toor S, Lindberg M, Falman I, Vallin A, Mohill O, Freyhult P, Nilsson L, Agback M, Viklund L, Zazzik H, et al. SNIC Science Cloud (SSC): a national-scale cloud infrastructure for Swedish academia. In: 2017 IEEE 13th International Conference on e-Science (e-Science); 24-27 Oct. 2017; 2017. p. 219–27.
Chapter
Google Scholar
Yu G, Champouret N, Steuernagel B, Olivera PD, Simmons J, Williams C, Johnson R, Moscou MJ, Hernandez-Pinzon I, Green P, et al. Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis. Theor Appl Genet. 2017;130:1207–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang S, Steffenson BJ, Sela H, Stinebaugh K. Resistance of Aegilops longissima to the rusts of wheat. Plant Dis. 2018;102:1124–35.
Article
PubMed
Google Scholar
Bauer E, Schmutzer T, Barilar I, Mascher M, Gundlach H, Martis MM, Twardziok SO, Hackauf B, Gordillo A, Wilde P, et al. Towards a whole-genome sequence for rye (Secale cereale L.). Plant J. 2017;89:853–69.
Article
CAS
PubMed
Google Scholar
Geiger H, Miedaner T. Rye breeding. Cereals. 2009;3:157–81.
Article
Google Scholar
Hirsch CN, Hirsch CD, Brohammer AB, Bowman MJ, Soifer I, Barad O, Shem-Tov D, Baruch K, Lu F, Hernandez AG, et al. Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize. Plant Cell. 2016;28:2700–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Unterseer S, Seidel MA, Bauer E, Haberer G, Hochholdinger F, Opitz N, Marcon C, Baruch K, Spannagl M, Mayer KFX, Schön C-C. European Flint reference sequences complement the maize pan-genome. bioRxiv. 2017:103747. https://doi.org/10.1101/103747.
Springer NM, Anderson SN, Andorf CM, Ahern KR, Bai F, Barad O, Barbazuk WB, Bass HW, Baruch K, Ben-Zvi G, et al. The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat Genet. 2018;50:1282–8.
Article
CAS
PubMed
Google Scholar
Thind AK, Wicker T, Simkova H, Fossati D, Moullet O, Brabant C, Vrana J, Dolezel J, Krattinger SG. Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly. Nat Biotechnol. 2017;35:793–6.
Article
CAS
PubMed
Google Scholar
Wendler N, Mascher M, Himmelbach A, Johnston P, Pickering R, Stein N. Bulbosum to go: a toolbox to utilize Hordeum vulgare/bulbosum introgressions for breeding and beyond. Mol Plant. 2015;8:1507–19.
Article
CAS
PubMed
Google Scholar
Xue S, Kolmer JA, Wang S, Yan L. Mapping of leaf rust resistance genes and molecular characterization of the 2NS/2AS translocation in the wheat cultivar jagger. G3 (Bethesda). 2018;8:2059–65.
Article
CAS
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
CAS
PubMed
PubMed Central
Google Scholar
Benoit G, Lavenier D, Lemaitre C, Rizk G. Bloocoo, a memory efficient read corrector. In: European Conference on Computational Biology (ECCB); 2014-09-07; Strasbourg, France; 2014.
Google Scholar
Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS, et al. Improved maize reference genome with single-molecule technologies. Nature. 2017;546:524–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schmidt MH, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Mass J, Pfaff C, et al. De novo assembly of a new Solanum pennellii accession using nanopore sequencing. Plant Cell. 2017;29:2336–48.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang M, Tu L, Yuan D, Zhu SC, Li J, Liu F, Pei L, Wang P, Zhao G, et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nat Genet. 2019;51:224–9.
Article
CAS
PubMed
Google Scholar
Wenger AM, Peluso P, Rowell WJ, Chang P-C, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, et al. Highly-accurate long-read sequencing improves variant detection and assembly of a human genome.Nat Biotechnol. 2019;37:1155–62. https://doi.org/10.1038/s41587-019-0217-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Csardi G, Nepusz T. The igraph software package for complex network research. InterJ Complex Syst. 2006;1695:1–9.
Google Scholar
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv. 2013:13033997.
Hu M, Deng K, Selvaraj S, Qin Z, Ren B, Liu JS. HiCNorm: removing biases in Hi-C data via Poisson regression. Bioinformatics. 2012;28:3131–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gremme G, Brendel V, Sparks ME, Kurtz S. Engineering a software tool for gene structure prediction in higher organisms. Inf Softw Technol. 2005;47:965–78.
Article
Google Scholar
Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12:357–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33:290–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ghosh S, Chan CK. Analysis of RNA-Seq data using TopHat and Cufflinks. Methods Mol Biol. 2016;1374:339–61.
Article
CAS
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Article
CAS
PubMed
Google Scholar
Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 2011;7:e1002195.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stanke M, Schoffmann O, Morgenstern B, Waack S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics. 2006;7:62.
Article
PubMed
PubMed Central
CAS
Google Scholar
Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008;9:R7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Spannagl M, Nussbaumer T, Bader KC, Martis MM, Seidel M, Kugler KG, Gundlach H, Mayer KF. PGSB PlantsDB: updates to the database framework for comparative plant genome research. Nucleic Acids Res. 2016;44:D1141–7.
Article
CAS
PubMed
Google Scholar
Ellinghaus D, Kurtz S, Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics. 2008;9:18.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mistry J, Finn RD, Eddy SR, Bateman A, Punta M. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res. 2013;41:e121.
Article
CAS
PubMed
PubMed Central
Google Scholar
SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. The paleontology of intergene retrotransposons of maize. Nat Genet. 1998;20:43–5.
Article
CAS
PubMed
Google Scholar
Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kurtz S, Narechania A, Stein JC, Ware D. A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics. 2008;9:517.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wicker T, Yu Y, Haberer G, Mayer KF, Marri PR, Rounsley S, Chen M, Zuccolo A, Panaud O, Wing RA, Roffler S. DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses. Nat Commun. 2016;7:12790.
Article
PubMed
PubMed Central
Google Scholar
Mascher M. Source of the TRITEX assembly pipeline. Bitbucket. 2019; https://bitbucket.org/tritexassembly/tritexassembly.bitbucket.io. Accessed 10 Dec 2019.
Mascher M: Source of the TRITEX assembly pipeline. e!DAL - Plant Genomics & Phenomics Research Data Repository 2019, doi: https://doi.org/10.5447/IPK/2019/19. Accessed 10 Dec 2019.
Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, et al: Paired-end, mate-pair, 10X and Chicago data generated for barley cv. Morex. EMBL ENA 2019, https://www.ebi.ac.uk/ena/data/view/PRJEB31444. Accessed 10 Dec 2019.
Arend D, Junker A, Scholz U, Schüler D, Wylie J, Lange M. PGP repository: a plant phenomics and genomics data publication infrastructure. Database (Oxford). 2016 Apr 17;2016. pii: baw033. https://doi.org/10.1093/database/baw033.
Article
PubMed
PubMed Central
Google Scholar
Arend D, Lange M, Chen J, Colmsee C, Flemming S, Hecht D, Scholz U. e! DAL-a framework to store, share and publish research data. BMC bioinformatics. 2014;15:214.
Article
PubMed
PubMed Central
Google Scholar
Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, et al. TRITEX assembly of wild emmer Zavitan. EMBL ENA. 2019; https://www.ebi.ac.uk/ena/data/view/CACRSD010000000. Accessed 10 Dec 2019.
Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, et al: TRITEX assembly of bread wheat cv. Chinese Spring. EMBL ENA 2019, https://www.ebi.ac.uk/ena/data/view/CACRSF010000000.
Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, et al: Morex V2 pseudomolecules EMBL ENA 2019, https://www.ebi.ac.uk/ena/data/view/PRJEB34496&portal=sequence_update. Accessed 10 Dec 2019.
Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, et al: Dovetail assembly of barley cv. Morex. EMBL ENA 2019, https://www.ebi.ac.uk/ena/data/view/CABWKO010000000. Accessed 10 Dec 2019.
Tange O. Gnu parallel-the command-line power tool. USENIX Magazine. 2011;36:42–7.
Google Scholar