Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

[61] Kondo T(2012)Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules Nat Methods 9 357-undefined

[62] Takata K(2012)Fast gapped-read alignment with bowtie 2 BMC Bioinformatics 13 238-undefined

[63] Chumley TW(2011)Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory Mol Ecol Resour 11 759-undefined

[64] Palmer JD(2012)Field guide to next-generation DNA sequencers J Comput Biol 19 455-undefined

[65] Mower JP(2015)SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing Bioinformatics 31 3421-undefined

[66] Fourcade HM(2017)Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data BMC Bioinformatics 18 374-undefined

[67] Calie PJ(2017)Evaluation of the impact of Illumina error correction tools on de novo genome assembly Nucleic Acids Res 45 e18-undefined

[68] Boore JL(2004)NOVOPlasty: de novo assembly of organelle genomes from whole genome data Genome Biol 5 R12-undefined

[69] Shinozaki K(2014)Versatile and open software for comparing large genomes PLoS One 9 e112963-undefined

[70] Ohme M(2015)Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement Nat Methods 12 733-undefined

[61] Kondo T(2012)Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules Nat Methods 9 357-undefined

[62] Takata K(2012)Fast gapped-read alignment with bowtie 2 BMC Bioinformatics 13 238-undefined

[63] Chumley TW(2011)Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory Mol Ecol Resour 11 759-undefined

[64] Palmer JD(2012)Field guide to next-generation DNA sequencers J Comput Biol 19 455-undefined

[65] Mower JP(2015)SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing Bioinformatics 31 3421-undefined

[66] Fourcade HM(2017)Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data BMC Bioinformatics 18 374-undefined

[67] Calie PJ(2017)Evaluation of the impact of Illumina error correction tools on de novo genome assembly Nucleic Acids Res 45 e18-undefined

[68] Boore JL(2004)NOVOPlasty: de novo assembly of organelle genomes from whole genome data Genome Biol 5 R12-undefined

[69] Shinozaki K(2014)Versatile and open software for comparing large genomes PLoS One 9 e112963-undefined

[70] Ohme M(2015)Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement Nat Methods 12 733-undefined