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LoRDEC: hybrid correction of long reads lordec_logo.png

Table of Contents

Date : 09-09-2020

News

LoRDEC has been accepted by the Elixir Service Delivery Plan in 2019. LoRDEC is now registered in the ELIXIR bio.tools database (https://bio.tools/ under this entry), and documented following the EDAM ontology. Elixir is a European organisation that coordinates life science resources from across Europe, and the Institut Français de Bioinformatique is the French node of Elixir.

Elixir logo

Overview

LoRDEC is a bioinformatics software developed in 2014 at the CNRS, Université de Montpellier (France) in collaboration with Leena Salmela of University of Helsinki (Finland).
LoRDEC processes data coming from high throughput sequencing machines of the second and third generations. These data are called sequencing reads, or simply reads for short. Technically speaking it processes short reads and long reads to correct errors in the long reads.

Third generation DNA sequencing technologies yield long, but error rich sequencing reads, while second generation technologies yield short read with low error rate. Hence, the need for correcting the long reads.

LoRDEC is a program for error correcting long sequencing reads using short reads. It implements a hybrid correction approach. It uses little memory and is very efficient. Most importantly it scales up to process very large data sets. It can be applied to long reads obtained with either Pacific Biosciences SMRT sequencing (SMRT = Single Molecule Real Time) or with Oxford Nanopore MINion technology.

This page maintains up to date information about LoRDEC software, including a table of completed genomic and transcriptomic projects (Table 1), with their distribution grouped by species (Figure 2) and by country (Figure 3).

lordec-species.png

Figure 2: Genomic and transcriptomic projects using LoRDEC (as of 2020-09-01).

lordec-country.png

Figure 3: Genomic and transcriptomic projects using LoRDEC (as of 2019-09-01).

Elixir catalog: https://bio.tools/lordec

Frequently Asked Questions (FAQ): it's here.

Publication

The algorithm, the software, and its performances are described in
LoRDEC: accurate and efficient long read error correction
L. Salmela and E. Rivals
Bioinformatics 30(24):3506-3514, 2014, doi: 10.1093/bioinformatics/btu538.

For citations: on G. Scholar, on CrossRef, or on Scopus

Getting the program for Linux or MacOSX

Completed genome / transcriptome projects that used LoRDEC

We record completed projects that explicitely used LoRDEC for read correction and are associated with an available publication (as of 01-09-2020)
A total of 93 projects have been completed and published. If you are aware of more send us an email (lordec@lirmm.fr).

Legends for group species: A: animals, B: bacteria, F: fungi, H: human, V: viruses, E: other eukaryotes i.e. protists.

Number Species Type Journal DOI Year Country Comments Speciesgroup
1 tree Azadirachta indica genome G3: Genes, Genomes, Genetics https://doi.org/10.1534/g3.116.030056 2016 India evergreen tree, Meliaceae family, medicinal, pesticidal & insecticidal properties; company P
2 sorghum Sorghum bicolor BTx623 genotype transcriptome Nature Communications http://dx.doi.org/10.1038/ncomms11706 2016 USA important bioenergy crop; TAPIS pipeline P
3 rabbit Oryctolagus cuniculus transcriptome Scientific Reports https://doi.org/10.1038/s41598-017-08138-z 2017 China provides meat, fur and wool products worldwide A
4 strawberry Fragaria vesca transcriptome The Plant Journal https://doi.org/10.1111/tpj.13462 2016 / 2017 China wild strawberry (diploid) Fragaria vesca, fruit crop of nutrition & economic value P
5 fungus Bipolaris cookei genome Scientific Reports https://doi.org/10.1038/s41598-017-17476-x 2017 USA pathogene sorghum F
6 butterfly Heliconius erato genome Nature Ecology & Evolution https://doi.org/10.1038/s41559-016-0052 2017 Finland evolution A
7 fungus Stenocarpella maydis genome Fungal Biology https://doi.org/10.1016/j.funbio.2017.08.006 2017 USA plant pathogenic fungus; causes Diplodia ear rot F
8 wheat Triticum aestivum genome Scientific Reports https://doi.org/10.1038/srep44609 2017 China hexaploid bread wheat, accounts for over 95% of global wheat production P
9 cacao Theobroma cacao L. Criollo genome BMC Genomics https://doi.org/10.1186/s12864-017-4120-9 2017 France with ATGC PF ; economically important fruit tree crop for tropical countries P
10 sugarcane Saccharum officinarum S. spontaneum transcriptome BMC Genomics https://doi.org/10.1186/s12864-017-3757-8 2017 Australia economic importance of sugarcane in sugar and bioenergy production P
11 strawberry Fragaria vesca transcriptome DNA Research https://doi.org/10.1093/dnares/dsx038 2018 China crop P
12 fungus Pochonia chlamydosporia genome secretome Scientific Reports https://doi.org/10.1038/s41598-018-19169-5 2018 China P. chlamydosporia infects eggs and females of economically important plant-parasitic nematodes F
13 chicken Gallus gallus domesticus genome transcriptome GigaScience https://doi.org/10.1093/gigascience/giy086 2018 Korea black native Korean chicken breed Yeonsan Ogye A
14 Western poplar Populus trichocarpa transcriptome Frontiers in Plant Science https://doi.org/10.3389/fpls.2018.00005 2018 USA tree P
15 peanut Arachis monticola genome GigaScience https://doi.org/10.1093/gigascience/giy066 2018 China wild plant; allotetraploid genome P
16 herb Sophora japonica genome PlOS One https://doi.org/10.1371/journal.pone.0202485 2018 China mitochondrial; traditional herb P
17 fungus Candida albicans genome Genome Biology and Evolution https://doi.org/10.1093/gbe/evy166 2018 Japan strain TIMM 1768; company F
18 bat Rousettus aegyptiacus genome Cell https://doi.org/10.1016/j.cell.2018.03.070 2018 USA army; medical; Egyptian Roussete A
19 Chinese hamster Cricetulus griseus genome Biotechnology and Bioengineering https://doi.org/10.1002/bit.26722 2018 USA ; Austria biotech species for exogenous protein production A
20 bermudagrass Cynodon dactylon (L.) Pers. transcriptome Plant Physiology and Biochemistry https://doi.org/10.1016/j.plaphy.2018.08.039 2018 China Cynodon dactylon (L.) Pers.; turfgrass; economic value P
21 tree poplar Populus bolleana Populus alba genome Plant Biotechnology Journal https://doi.org/10.1111/pbi.12989 2018 China var. pyramidalis; economic interest short transformation time P
22 bacteria Staphylococcus aureus genome Microbiology Resource Announcements https://doi.org/10.1128/MRA.00892-18 2018 Canada strains CMRSA3 & CMRSA6; Methicillin-resistant B
23 caddisfly Stenopsyche tienmushanensis genome GigaScience https://doi.org/10.1093/gigascience/giy143 2018 China species widely employed as bio-indicators in water quality assessment and monitoring. A
24 jellyfish medusa Tripedalia cystophora transcriptome BMC Genomics https://doi.org/10.1186/s12864-019-5514-7 2019 Denmark nervous system development, evolution, neuropeptides A
25 grape Berry (C. sauvignon) transcriptome G3: Genes, Genomes, Genetics https://doi.org/10.1534/g3.118.201008 2019 USA economically crucial grape cultivar P
26 shrimp Litopenaeus vannamei transcriptome Fish & Shellfish Immunology https://doi.org/10.1016/j.fsi.2019.01.023 2019 China economically important shrimp for aquaculture industry A
27 Crustacea Armadillidium vulgare genome Molecular Biology and Evolution https://doi.org/10.1093/molbev/msz010 2019 France evolution sex chromosome A
28 golden algae Hydrurus foetidus genome F1000 Research https://doi.org/10.12688/f1000research.16734.1 2019 Norway evolution and ecological roles of chrysophyte algae P
29 rapeseed Brassica napus genome Plant Biotechnology Journal https://doi.org/10.1111/pbi.13115 2019 China B napus (AACC, 2n=38) important oilseed crop grown worldwide P
30 Paper Mulberry Broussonetia papyrifera genome Molecular Plant https://doi.org/10.1016/j.molp.2019.01.021 2019 China papermaking, forage plant P
31 grape Carménère genome G3: Genes, Genomes, Genetics https://doi.org/10.1534/g3.119.400030 2019 USA economically crucial grape cultivar P
32 birds Zosterops borbonicus, Z. pallidus genome bioRxiv http://dx.doi.org/10.1101/505610 2018 France evolution sex chromosome A
33 locust Locusta migratoria transcriptome RNA Biology https://doi.org/10.1080/15476286.2019.1602437 2019 China economically important threat to agriculture A
34 Opium poppy Papaver somniferum transcriptome Scientific Data https://doi.org/10.1038/s41597-019-0082-x 2019 China medicinal plants, only commercial resource of morphinan-based painkillers P
35 Kaposi sarcoma-associated herpesvirus genome J. of Virology https://doi.org/10.1128/JVI.00630-19 2019 USA medical V
36 pepper Capsicum annuum transcriptome The Plant Journal https://doi.org/10.1111/tpj.14351 2019 China economically important P
37 Human breast cancer transcriptome Scientific Reports https://doi.org/10.1038/s41598-019-42184-z 2019 China health H
38 Lotus Nelumbo nucifera transcriptome DNA Research https://doi.org/10.1093/dnares/dsz010 2019 China important aquatic horticultural plant P
39 common morning glory Ipomoea purpurea exome Biorxiv https://doi.org/10.1101/647164 2019 USA common agricultural weed P
40 Red maple Acer rubrum L. transcriptome BMC Plant Biology https://doi.org/10.1186/s12870-019-1850-7 2019 China economically important P
41 Indian mithun Bos frontalis genome BMC Genomics https://doi.org/10.1186/s12864-019-5980-y 2019 India ; Denmark agriculture A
42 Esophageal squamous cell carcinoma transcriptome Frontiers in Genetics https://doi.org/10.3389/fgene.2019.00915 2019 China health H
43 Leucobacter metagenomics BMC Genomics https://doi.org/10.1186/s12864-019-6206-z 2019 Portugal metabolic collaboration B
44 brown plan hopper Nilaparvata lugens transcriptome BMC Genomics https://doi.org/10.1186/s12864-019-6049-7 2019 China pest of rice A
45 Mycobacterium bovis genome BMC Genomics https://doi.org/10.1186/s12864-019-5909-5 2019 Belgium tuberculosis vaccine B
46 mouse Mus musculus transcriptome BMC Genomics https://doi.org/10.1186/s12864-019-5903-y 2019 USA ; China retinal development A
47 giant grouper (Epinephelus lanceolatus genome Marine Drugs https://doi.org/10.3390/md17090503 2019 China economically important A
48 Weissella hellenica genome Frontiers in Microbiology https://doi.org/10.3389/fmicb.2019.01619 2019 Japan fermenting bacteria B
49 yellowthorn Xanthoceras sorbifolium transcriptome GigaScience https://doi.org/10.1093/gigascience/giz070 2019 China economically important P
50 Schistosoma haematobium genome GigaScience https://doi.org/10.1093/gigascience/giz108 2019 Australia health, human parasite A
51 Chinese rhesus macaque Macaca mulatta transcriptome Nature Communications https://doi.org/10.1038/s41467-019-12174-w 2019 China most widely studied nonhuman primate A
52 Armadillidium vulgare genome Molecular Biology and Evolution https://doi.org/10.1093/molbev/msz010 2019 France model species for sex determination and symboiosis in animals A
53 mud crab Scylla paramamosain transcriptome Aquaculture https://doi.org/10.1016/j.aquaculture.2019.734447 2019 China economically important A
54 Teratosphaeria gauchensis genome IMA Fungus https://doi.org/10.1186/s43008-019-0013-7 2019 South Africa plant pathogen F
55 seagrass Zostera japonica transcriptome Scientific Reports https://doi.org/10.1038/s41598-019-51176-y 2019 China ecology P
56 redlip mullet Liza haematocheila genome Frontiers in Genetics https://doi.org/10.3389/fgene.2019.01246 2019 South Korea cultivated fish A
57 duck Anas platyrhynchos transcriptome Scientific Data https://doi.org/10.1038/s41597-019-0293-1 2019 China economically important A
58 superb fairy-wren Malurus cyaneus genome Molecular Ecology Resources https://doi.org/10.1111/1755-0998.13124 2020 Germany ; Australia evolution, endemic Australian bird A
59 Boehmeria tricuspis transcriptome International Journal of Genomics https://doi.org/10.1155/2019/4025747 2019 China asexual reproduction P
60 Pseudotaxus chienii transcriptome International Journal of Molecular Sciences https://doi.org/10.3390/ijms21124305 2020 China ecological and economical value P
61 pitaya Hylocereus transcriptome International Journal of Molecular Sciences https://doi.org/10.3390/ijms21093288 2020 China agriculture P
62 poplar Populus alba transcriptome Frontiers in Genetics https://doi.org/10.3389/fgene.2020.00048 2020 China economically important P
63 pacific white shrimp Litopenaeus vannamei transcriptome Frontiers in Genetics https://doi.org/10.3389/fgene.2020.00071 and https://doi.org/10.1016/j.fsi.2019.01.023 2019 / 2020 China economically important A
64 Phakopsora pachyrhizi transcriptome Physiological and Molecular Plant Pathology https://doi.org/10.1016/j.pmpp.2020.101464 2020 USA soybean pathogen F
65 crabapple Malus spp. transcriptome Plant Physiology and Biochemistry https://doi.org/10.1016/j.plaphy.2020.01.033 2020 China gardening and landscaping P
66 Cupressus chengiana transcriptome Molecular Ecology https://doi.org/10.1111/mec.15407 2020 China ecology P
67 human adenovirus type 5 transcriptome Communications Biology https://doi.org/10.1038/s42003-020-0849-9 2020 UK health V
68 oilseed rape Brassica napus transcriptome The Plant Journal https://doi.org/10.1111/tpj.14754 2020 China economically important P
69 alpine grass Stipa capillacea and Stipa purpurea transcriptome Journal of Experimental Botany https://doi.org/10.1093/jxb/eraa194 2020 China evolution P
70 Rhododendron delavayi genome PeerJ https://doi.org/10.7717/peerj.9048 2020 China gardening and landscaping P
71 ramie Boehmeria nivea L. Gaudich transcriptome Industrial Crops and Products https://doi.org/10.1016/j.indcrop.2020.112544 2020 China economically important P
72 red palm weevil Rhynchophorus ferrugineus transcriptome PeerJ https://doi.org/10.7717/peerj.9133 2020 China palm tree pest A
73 thraustochytrid Aurantiochytrium limacinum genome Data in Brief https://doi.org/10.1016/j.dib.2020.105729 2020 France industrial production E
74 Penium margaritaceum transcriptome Cell https://doi.org/10.1016/j.cell.2020.04.019 2020 USA evolution P
75 razor clam Sinonovacula constricta transcriptome Frontiers in Genetics https://doi.org/10.3389/fgene.2020.00664 2020 China economically important A
76 Litchi Litchi chinensis Sonn. transcriptome Postharves Biology and Technology https://doi.org/10.1016/j.postharvbio.2020.111252 2020 China economically important P
77 hybrid: blunt snout bread x topmouth culter Megalobramaamblycephala x Culter alburnus transcriptome BMC Genomics https://doi.org/10.1186/s12864-020-06866-7 2020 China maternal effects on transcription A
78 Armillaria gallica 012m genome Brazilian Journal of Microbiology https://doi.org/10.1007/s42770-020-00317-x 2020 China plant disease B
79 kuruma shrimp Marsupenaeus japonicus transcriptome Fish and Shellfish Immunology https://doi.org/10.1016/j.fsi.2020.07.018 2020 China economically important A
80 tall fescue Festuca arundinacea transcriptome BMC Plant Biology https://doi.org/10.1186/s12870-020-02572-4 2020 China agriculture P
81 ticks Acari: Ixodidae genome Cell https://doi.org/10.1016/j.cell.2020.07.023 2020 China health A
82 soil bacteria Mesorhizobium genome Microbial Genomics https://doi.org/10.1099/mgen.0.000426 2020 New Zealand ; Australia nitrogen binding B
83 human breast cancer transcriptome bioRxiv https://doi.org/10.1101/2020.07.15.199851 2020 Japan health H
84 macadamia Macadamia integrifolia genome bioRxiv https://doi.org/10.1101/2020.05.25.114009 2020 Australia agriculture P
85 Tripterygium wilfordii transcriptome bioRxiv https://doi.org/10.1101/2020.06.29.176958 2020 China traditional chinese medicine, medical value P
86 Ascosphaera apis transcriptome bioRxiv https://doi.org/10.1101/2020.03.19.998625 2020 China fungal disease of honeybees F
87 C. elegans microbiome metagenomics bioRxiv https://doi.org/10.1101/2020.04.22.055426 2020 Germany ; USA model species microbiome B
88 Hard Fescue Turfgrass Festuca brevipila transcriptome bioRxiv https://doi.org/10.1101/2020.02.26.966952doi 2020 USA gardening and landscaping P
89 Stevia rebaudiana transcriptome Research Square https://doi.org/10.21203/rs.3.rs-24957/v2 2020 China economically important P
90 Sea vomit Didemnum vexillum genome Research Square https://doi.org/10.21203/rs.3.rs-23360/v1 2020 Colombia ; Germany evolution A
91 Liriodendron chinense (Hemsl.) Sarg. transcriptome Research Square https://doi.org/10.21203/rs.3.rs-32884/v1 2020 China economically important P
92 Gnetum transcriptome Research Square https://doi.org/10.21203/rs.3.rs-36058/v1 2020 China economically important P
93 wild apple Malus sieversii transcriptome Research Square https://doi.org/10.21203/rs.3.rs-47953/v1 2020 China plant disease P

Contacts

  • To contact us about LoRDEC please use: lordec@lirmm.fr
  • We have a list to contact regular users: lordec-users@lirmm.fr

Authors

  • Leena Salmela Department of Computer Science, P. O. Box 68, FIN-00014 University of Helsinki, Finland
  • Eric Rivals LIRMM and Institut de Biologie Computationelle, CNRS and Université Montpellier, Montpellier, France

Contributors: Julien Veyssier LIRMM, CNRS and Université Montpellier, Montpellier, France

Acknowledgements and supports

We thank :

  • Erwan Drezen (GATB team)
  • Yvan Le Bras (GenOuest platform)
  • Vincent Lefort (LIRMM ATGC plaftorm)
  • Cyril Monjeaud (Plate-form GenOuest)
  • Dominique Lavenier (IRISA Rennes)
  • all authors of GATB library
  • Amal Makrini (LIRMM ATGC plaftorm)

Supports:

cnrs-logo.png helsinki-logo.png ibc_logo_200.png ifb-logo.png

Author: Eric Rivals

Created: 2020-09-09 mer. 16:01

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