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Benchmark Test of Organelle Genome Assembly Using GetOrganelle

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GetOrganelleComparison

This repository aims to make all our tests/comparisons reproducible. These mainly include:

  • Comparisons among published plastomes, plastomes re-assembled using GetOrganelle v1.6.2, and plastomes re-assembled using NOVOPlasty v2.7.2.
  • Comparisons between the animal/fungal mitogenomes assembled using GetOrganelle v1.6.2 and NOVOPlasty v2.7.2.
  • Performance characteristics of GetOrganelle using different parameters.

Preparing

If you want to reproduce our results on your own computer, please

  • Download (clone) files in GetOrganelleComparison/bin (ca. 23Mb uncompressed) using

    svn co https://github.com/Kinggerm/GetOrganelleComparison/trunk/bin

    or clone the entire repository (ca. 1.9Gb uncompressed)

    git clone git://github.com/Kinggerm/GetOrganelleComparison

  • Download the dataset (see Samples) using 1.downloading_data.sh inside the downloaded GetOrganelleComparison/bin.

  • Download and install GetOrganelle v1.6.2** as well as its dependencies (instruction). NOVOPlasty v2.7.2 is included in GetOrganelleComparison/bin and not needed to be specifically installed.

Running

After finishing the Preparing, you can follow the following lines to reproduce our results.

Extra tests:

Results

A simplified assembly results of GetOrganelle, NOVOPlasty and/or Published were deposited in GetOrganelleComparison/res.

A simplified evaluation results for GetOrganelle, NOVOPlasty and/or Published were deposited in GetOrganelleComparison/eval.

Sample Info

50 Plant Datasets

We selected 50 samples of vascular plants with raw reads achieved in the database of Sequence Reads Archive (SRA). Raw reads of the 50 samples are associated with published plastome, which provided a great opportunity to compare the differences between the published plastome and the newly reassembled plastomes. In the all tests, if the tested data less than 10,000,00 reads for each end, we used all the reads; if the data was more than 10,000,000 reads of each end, we only select the first 10,000,000 reads for each ends.

Major Clade/Grade Order Family Species SRA RunID Sequecing plastform Read length (bp) Published Accession No.
Lycopodiopsida Selaginellales Selaginellaceae Selaginella kraussiana (Kunze) A. Braun SRR2037123 HiSeq 2000 2*100 MH549643.1
Polypodiopsida Salviniales Salviniaceae Azolla filiculoides Lam. SRR6932851 HiSeq 2000 2*100 MF177094.1
Polypodiopsida Salviniales Salviniaceae Salvinia cucullata Roxb. SRR6478596 HiSeq 2000 2*125 MF177095.1
Polypodiopsida Ophioglossales Ophioglossaceae Mankyua chejuensis B.Y.Sun, M.H.Kim & C.H.Kim SRR7630500 MiSeq 2*300 KP205433.1
Ginkgophyta Ginkgoales Ginkgoaceae Ginkgo biloba L. ERR2206741 HiSeq 2000 2*100 MG922595.1
Pinophyta Cupressales Cupressaceae Juniperus cedrus Webb & Berthel. SRR1145775 HiSeq 2000 2*100 KT378453.1
Pinophyta Pinales Pinaceae Picea abies (L.) H. Karst. ERR268390 HiSeq 2000 2*100 HF937082.1
Pinophyta Pinales Pinaceae Picea sitchensis (Bong.) Carrière SRR5028199 HiSeq X Ten 2*150 KU215903.2
ANA Grade Austrobaileyales Schisandraceae Illicium anisatum L. SRR5602608 MiSeq 2*250 KY085919.1
ANA Grade Austrobaileyales Schisandraceae Illicium floridanum J. Ellis SRR5602609 MiSeq 2*300 KY085892.1
ANA Grade Austrobaileyales Schisandraceae Illicium henryi Diels SRR5602610 MiSeq 2*300 KY085910.1
ANA Grade Austrobaileyales Schisandraceae Illicium verum Hook. f. SRR5602607 MiSeq 2*250 KY085896.1
Magnoliids Laurales Lauraceae Laurus nobilis L. SRR5602602 MiSeq 2*300 KY085912.1
Magnoliids Magnoliales Magnoliaceae Magnolia biondii Pamp. SRR5602588 MiSeq 2*300 KY085894.1
Magnoliids Magnoliales Magnoliaceae Magnolia denudata Desr. SRR5602603 MiSeq 2*300 KY085917.1
Magnoliids Magnoliales Magnoliaceae Magnolia officinalis Rehder & E.H. Wilson SRR5602589 MiSeq 2*300 KY085916.1
Monocots Asparagales Amaryllidaceae Allium sativum L. SRR5602598 MiSeq 2*300 KY085913.1
Monocots Dioscoreales Dioscoreaceae Dioscorea villosa L. SRR5602590 MiSeq 2*300 KY085893.1
Monocots Zingiberales Musaceae Musa balbisiana Colla SRR2057084 HiSeq 2000 2*100 KT595228.1
Basal Eudicots Ranunculales Ranunculaceae Actaea racemosa L. SRR5602599 MiSeq 2*250 KY085920.1
Basal Eudicots Ranunculales Ranunculaceae Hydrastis canadensis L. SRR5602606 MiSeq 2*250 KY085918.1
Fabids Rosales Rosaceae Eriobotrya japonica (Thunb.) Lindl. SRR5602604 MiSeq 2*250 KY085905.1
Fabids Rosales Rosaceae Fragaria virginiana Mill. SRR5602605 MiSeq 2*300 KY085911.1
Fabids Rosales Rosaceae Prunus dulcis (Mill.) D.A. Webb SRR5602582 MiSeq 2*300 KY085904.1
Malvids Malvales Cytinaceae Cytinus hypocistis (L.) L. ERR964904 HiSeq 2000 2*100 KT335971.1
Malvids Malvales Malvaceae Althaea officinalis L. SRR5602596 MiSeq 2*300 KY085914.1
Malvids Malvales Malvaceae Theobroma cacao L. SRR5602583 MiSeq 2*300 KY085907.1
Malvids Myrtales Myrtaceae Pimenta dioica (L.) Merr. SRR5602585 MiSeq 2*300 KY085891.1
Malvids Piperales Piperaceae Piper auritum Kunth SRR5602592 MiSeq 2*300 KY085906.1
Malvids Piperales Piperaceae Piper nigrum L. SRR5602591 MiSeq 2*300 KY085899.1
Malvids Sapindales Burseraceae Boswellia sacra Flueck. SRR5602594 MiSeq 2*300 KY085915.1
Malvids Sapindales Rutaceae Citrus limon (L.) Osbeck SRR5602593 MiSeq 2*250 KY085897.1
Campanulids Apiales Araliaceae Eleutherococcus senticosus (Rupr. ex Maxim.) Maxim. SRR5602586 MiSeq 2*300 KY085901.1
Campanulids Asterales Asteraceae Artemisia annua L. SRR5602595 MiSeq 2*250 KY085890.1
Campanulids Asterales Asteraceae Echinacea angustifolia DC. SRR5602579 MiSeq 2*300 KX548221.1
Campanulids Asterales Asteraceae Echinacea atrorubens (Nutt.) Nutt. SRR5602578 MiSeq 2*250 KX548220.1
Campanulids Asterales Asteraceae Echinacea laevigata (C.L. Boynton & Beadle) S.F. Blake SRR5602581 MiSeq 2*250 KX548219.1
Campanulids Asterales Asteraceae Echinacea paradoxa (Norton) Britton SRR5602575 MiSeq 2*300 KX548217.1
Campanulids Asterales Asteraceae Echinacea purpurea (L.) Moench SRR5602574 MiSeq 2*300 KX548224.1
Campanulids Asterales Asteraceae Echinacea sanguinea Nutt. SRR5602577 MiSeq 2*250 KX548225.1
Campanulids Asterales Asteraceae Echinacea speciosa Lindl. SRR5602576 MiSeq 2*250 KX548222.1
Campanulids Asterales Asteraceae Echinacea tennesseensis (Beadle) Small SRR5602587 MiSeq 2*250 KX548223.1
Lamiids Gentianales Rubiaceae Coffea arabica L. SRR5602572 MiSeq 2*300 KY085909.1
Lamiids Gentianales Rubiaceae Mitragyna speciosa (Korth.) Havil. SRR5602600 MiSeq 2*300 KY085908.1
Lamiids Lamiales Gesneriaceae Haberlea rhodopensis Friv. SRR4428742 HiSeq 2000 2*100 KX657870.1
Lamiids Lamiales Lamiaceae Scutellaria lateriflora L. SRR5602584 MiSeq 2*300 KY085900.1
Lamiids Lamiales Oleaceae Jasminum tortuosum Willd. SRR5602601 MiSeq 2*300 KY085898.1
Lamiids Lamiales Plantaginaceae Digitalis lanata Ehrh. SRR5602573 MiSeq 2*300 KY085895.1
Lamiids Lamiales Verbenaceae Aloysia citriodora Palau SRR5602597 MiSeq 2*300 KY085903.1
Lamiids Solanales Convolvulaceae Cuscuta campestris Yunck. ERR1917165 MiSeq 2*150 unpublished

50 Fungal Datasets

Division Class Orders Family Species SRA RunID Read length (bp)
Ascomycota Pezizomycetes Pezizales Morchellaceae Morchella eximia SRR5804017 2*150
Ascomycota Pezizomycetes Pezizales Morchellaceae Morchella septimelata SRR5804020 2*150
Ascomycota Pezizomycetes Pezizales Tuberaceae Tuber calosporum SRR5804115 2*150
Ascomycota Pezizomycetes Pezizales Tuberaceae Tuber microsphaerosporum SRR5804127 2*150
Ascomycota Pezizomycetes Pezizales Tuberaceae Tuber umbilicatum SRR5804118 2*150
Ascomycota Pezizomycotina Pezizales Morchellaceae Morchella septimelata SRR5804157 2*150
Ascomycota Sordariomycetes Xylariales Hypoxylaceae Annulohypoxylon stygiun SRR5804137 2*150
Basidiomycota Agaricomycetes Agaricales Agaricaceae Coprinus comatus SRR5804015 2*150
Basidiomycota Agaricomycetes Agaricales Agaricaceae Macrolepiota dolichaula SRR5801935 2*150
Basidiomycota Agaricomycetes Agaricales Amanitaceae Amanita pseudoporphyria SRR5804159 2*150
Basidiomycota Agaricomycetes Agaricales Bolbitiaceae Agrocybe cylindracea SRR5801932 2*150
Basidiomycota Agaricomycetes Agaricales Catathelasmataceae Catathelasma ventricosum SRR5802411 2*150
Basidiomycota Agaricomycetes Agaricales Hygrophoraceae Hygrophorus pudorinus SRR5803922 2*150
Basidiomycota Agaricomycetes Agaricales Hygrophoraceae Hygrophorus russula SRR5803933 2*150
Basidiomycota Agaricomycetes Agaricales Physalacriaceae Hymenopellis chiangmaiae SRR5803905 2*150
Basidiomycota Agaricomycetes Agaricales Tricholomataceae Collybia sp. SRR5802125 2*150
Basidiomycota Agaricomycetes Agaricales Tricholomataceae Megacollybia marginata SRR5803926 2*150
Basidiomycota Agaricomycetes Agaricales Tricholomataceae Tricholoma terreum SRR5802698 2*150
Basidiomycota Agaricomycetes Agaricales Tricholomataceae Tricoloma sp. SRR5804112 2*150
Basidiomycota Agaricomycetes Auriculariales Auriculariaceae Auricularia polytricha SRR5803923 2*150
Basidiomycota Agaricomycetes Boletales Boletaceae Boletus bicolor SRR5754079 2*150
Basidiomycota Agaricomycetes Boletales Boletaceae Boletus edulis SRR5764827 2*150
Basidiomycota Agaricomycetes Boletales Boletaceae Boletus sp. SRR5803909 2*150
Basidiomycota Agaricomycetes Boletales Boletaceae Boletus sp. SRR5804023 2*150
Basidiomycota Agaricomycetes Boletales Boletaceae Boletus speciosus SRR5765276 2*150
Basidiomycota Agaricomycetes Boletales Boletaceae Boletus subvelutipes SRR5801947 2*150
Basidiomycota Agaricomycetes Boletales Boletaceae Butyriboletus roseoflavus SRR5802181 2*150
Basidiomycota Agaricomycetes Boletales Boletaceae Caloboletus calopus SRR5801934 2*150
Basidiomycota Agaricomycetes Boletales Boletaceae Neoboletus brunneissimus SRR5764829 2*150
Basidiomycota Agaricomycetes Boletales Boletaceae Neoboletus magnificus SRR5801933 2*150
Basidiomycota Agaricomycetes Boletales Boletaceae Retiboletus ornatipes SRR5802419 2*150
Basidiomycota Agaricomycetes Boletales Gomphidiaceae Chroogomphus rutilus SRR5803916 2*150
Basidiomycota Agaricomycetes Cantharellales Cantharellaceae Cantharellus appalachiensis SRR5802413 2*150
Basidiomycota Agaricomycetes Cantharellales Cantharellaceae Cantharellus cibarius SRR5803930 2*150
Basidiomycota Agaricomycetes Cantharellales Cantharellaceae Craterellus lutescens SRR5804147 2*150
Basidiomycota Agaricomycetes Gomphales Gomphaceae Gomphus bonarii SRR5804153 2*150
Basidiomycota Agaricomycetes Gomphales Gomphaceae Gomphus sp. SRR5803890 2*150
Basidiomycota Agaricomycetes Polyporales Grifolaceae Grifola frondosa SRR5804018 2*150
Basidiomycota Agaricomycetes Polyporales Laetiporaceae Laetiporus sulphureus SRR5804139 2*150
Basidiomycota Agaricomycetes Russulales Albatrellaceae Albatrellus ellisii SRR5803913 2*150
Basidiomycota Agaricomycetes Russulales Albatrellaceae Albatrellus sp. SRR5804145 2*150
Basidiomycota Agaricomycetes Russulales Russulaceae Lactarius deliciosus SRR5765278 2*150
Basidiomycota Agaricomycetes Russulales Russulaceae Lactarius echinetus SRR5804131 2*150
Basidiomycota Agaricomycetes Russulales Russulaceae Lactarius hatsudake SRR5801929 2*150
Basidiomycota Agaricomycetes Russulales Russulaceae Lactarius indigo SRR5804120 2*150
Basidiomycota Agaricomycetes Russulales Russulaceae Lactarius orange SRR5804130 2*150
Basidiomycota Agaricomycetes Russulales Russulaceae Lactarius trivialis SRR5803928 2*150
Basidiomycota Agaricomycetes Russulales Russulaceae Lactarius volemus SRR5764835 2*150
Basidiomycota Agaricomycetes Russulales Russulaceae Lactifluus pinguis SRR5801943 2*150
Basidiomycota Agaricomycetes Russulales Russulaceae Lactifluus rugatus SRR5804119 2*150

56 Animal Datasets

The same as samples used in MitoZ paper.

Phylum Class Order Family Species SRA Run ID Read length (bp)
Arthropoda Arachnida Astigmata Pyroglyphidae Dermatophagoides farinae SRR3098386 2*95
Arthropoda Arachnida Astigmata Pyroglyphidae Dermatophagoides pteronyssinus SRR5863004 2*300
Arthropoda Arachnida Trombidiformes Tetranychidae Tetranychus urticae SRR1284940 2*100
Arthropoda Branchiopoda Diplostraca Daphniidae Daphnia magna SRR4340274 2*100
Arthropoda Branchiopoda Diplostraca Daphniidae Daphnia pulex SRR5875655 2*100
Arthropoda Branchiopoda Notostraca Triopsidae Triops cancriformis SRR4782254 2*265
Arthropoda Chilopoda Geophilomorpha Linotaeniidae Strigamia maritima SRR941879 2*95
Arthropoda Insecta Blattodea Ectobiidae Blattella germanica SRR1566160 2*100
Arthropoda Insecta Diptera Calliphoridae Lucilia cuprina SRR1200276 2*100
Arthropoda Insecta Diptera Cecidomyiidae Mayetiola destructor SRR136494 2*95
Arthropoda Insecta Diptera Culicidae Anopheles funestus SRR1055280 2*100
Arthropoda Insecta Diptera Culicidae Anopheles gambiae ERR1952738 2*150
Arthropoda Insecta Diptera Drosophilidae Drosophila sechellia SRR5860573 2*150
Arthropoda Insecta Diptera Drosophilidae Drosophila simulans SRR2132981 2*100
Arthropoda Insecta Diptera Drosophilidae Drosophila yakuba SRR2318706 2*100
Arthropoda Insecta Diptera Tephritidae Ceratitis capitata SRR847379 2*100
Arthropoda Insecta Hemiptera Aphalaridae Pachypsylla venusta SRR940268 2*100
Arthropoda Insecta Hemiptera Pentatomidae Halyomorpha halys SRR1298377 2*100
Arthropoda Insecta Hymenoptera Apidae Apis cerana DRR095708 2*100
Arthropoda Insecta Hymenoptera Cephidae Cephus cinctus SRR1946581 2*125
Arthropoda Insecta Hymenoptera Formicidae Solenopsis invicta SRR620242 2*100
Arthropoda Insecta Lepidoptera Crambidae Chilo suppressalis SRR611174 2*100
Arthropoda Insecta Lepidoptera Noctuidae Spodoptera litura SRR5132384 2*100
Arthropoda Insecta Lepidoptera Pieridae Pieris rapae SRR4339879 2*150
Arthropoda Insecta Orthoptera Acrididae Locusta migratoria SRR3953043 2*125
Arthropoda Insecta Thysanoptera Thripidae Frankliniella occidentalis SRR1300141 2*100
Arthropoda Malacostraca Decapoda Penaeidae Marsupenaeus japonicus SRR2179962 2*100
Arthropoda Malacostraca Decapoda Penaeidae Penaeus monodon SRR5620467 2*150
Arthropoda Maxillopoda Siphonostomatoida Caligidae Lepeophtheirus salmonis SRR1950515 2*100
Arthropoda Merostomata Xiphosura Limulidae Limulus polyphemus SRR3879971 2*100
Chordata Mammalia Carnivora Ailuridae Ailurus fulgens SRR2730309 2*100
Chordata Mammalia Carnivora Canidae Canis lupus familiaris ERR466754 2*100
Chordata Mammalia Carnivora Felidae Acinonyx jubatus SRR2737540 2*100
Chordata Mammalia Carnivora Felidae Panthera pardus SRR3041429 2*100
Chordata Mammalia Carnivora Felidae Panthera tigris SRR836315 2*100
Chordata Mammalia Carnivora Ursidae Ailuropoda melanoleuca SRR2717571 2*100
Chordata Mammalia Carnivora Ursidae Ursus arctos SRR5878339 2*100
Chordata Mammalia Cetacea Balaenopteridae Balaenoptera bonaerensis DRR014695 2*100
Chordata Mammalia Cetacea Eschrichtiidae Eschrichtius robustus SRR5495100 2*100
Chordata Mammalia Chiroptera Vespertilionidae Myotis lucifugus SRR5769010 2*120
Chordata Mammalia Lagomorpha Leporidae Oryctolagus cuniculus SRR5056303 2*100
Chordata Mammalia Laurasiatheria Camelidae Vicugna pacos SRR4095109 2*100
Chordata Mammalia Laurasiatheria Cervidae Cervus elaphus SRR955308 2*100
Chordata Mammalia Laurasiatheria Suidae Sus scrofa SRR1581065 2*100
Chordata Mammalia Primates Cercopithecidae Chlorocebus sabaeus SRR1822107 2*100
Chordata Mammalia Primates Cercopithecidae Rhinopithecus bieti SRR1041081 2*100
Chordata Mammalia Primates Cercopithecidae Rhinopithecus roxellana SRR1743021 2*100
Chordata Mammalia Primates Daubentoniidae Daubentonia madagascariensis SRR329682 2*100
Chordata Mammalia Primates Hominidae Homo sapiens SRR039541 2*100
Chordata Mammalia Primates Hominidae Pan paniscus SRR747928 2*100
Chordata Mammalia Primates Hominidae Pongo abelii SRR748049 2*100
Chordata Mammalia Primates Indriidae Propithecus coquereli SRR1657027 2*100
Chordata Mammalia Rodentia Cricetidae Myodes glareolus SRR5201683 2*100
Chordata Mammalia Rodentia Muridae Meriones unguiculatus SRR5527082 2*150
Chordata Mammalia Rodentia Muridae Mus musculus ERR1856354 2*100
Chordata Mammalia Rodentia Sciuridae Ictidomys tridecemlineatus SRR305235 2*100

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Benchmark Test of Organelle Genome Assembly Using GetOrganelle

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GetOrganelleComparison v1.1.1 Latest
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