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Number of citations per year for the bioinformatics software tool LoRDEC
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LoRDEC specifications

Information


Unique identifier OMICS_05407
Name LoRDEC
Alternative name Long Read DBG Error Correction
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Pacific Biosciences
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Version 1.3.2
Stability Stable
Maintained Yes

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Versioning


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Maintainer


  • person_outline LoRDEC Team

Additional information


https://gite.lirmm.fr/lordec/lordec-releases/wikis/home

Publication for Long Read DBG Error Correction

LoRDEC citations

 (12)
library_books

Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching

2018
Front Plant Sci
PMCID: 5816337
PMID: 29483921
DOI: 10.3389/fpls.2018.00005

[…] Analysis software from Pacific Biosciences that did not exhibit an identifiable poly-(A) tail and 3′ adapter were removed. Finally, Iso-Seq reads were corrected using a hybrid error correction method LoRDEC () against a de Bruijn graph constructed from the bulk of RNA-Seq libraries (approximately 109 of 101 nt paired-end RNA-Seq reads, see above). These corrected Iso-Seq reads were further aligned […]

library_books

Genome and secretome analysis of Pochonia chlamydosporia provide new insight into egg parasitic mechanisms

2018
Sci Rep
PMCID: 5773674
PMID: 29348510
DOI: 10.1038/s41598-018-19169-5

[…] ree libraries of Illumina HiSeq 2000 sequencing reads by BGI-Shenzhen (China). Step 2: For four SMRT cells of PacBio RS long reads (Supplementary Table ), we performed error correction analysis using LoRDEC, and these corrected reads were used for the following analyses. We used SSPACE-LongRead to build scaffolds for Allpaths-LG-assembled contigs. The conflicting scaffolds between Allpaths-LG and […]

library_books

Isoform Sequencing and State of Art Applications for Unravelling Complexity of Plant Transcriptomes

2018
Genes
PMCID: 5793194
PMID: 29346292
DOI: 10.3390/genes9010043

[…] ce, LSC corrects 100,000 PacBio long reads by using 64 million short reads and reduces the error rate by more than three-fold in the transcript sequencing of human brain cerebellum []. The program of LoRDEC runs six times faster and requires 93% less memory than PacBioToCA and LSC, achieving a comparable accuracy []. The proovread program performs better than PacBioToCA and LSC by the tests of gen […]

library_books

The genome sequence of Bipolaris cookei reveals mechanisms of pathogenesis underlying target leaf spot of sorghum

2017
Sci Rep
PMCID: 5722872
PMID: 29222463
DOI: 10.1038/s41598-017-17476-x

[…] n a custom hybrid strategy (Supplementary Fig. ). The Illumina reads were corrected with Bayes Hammer within SPAdes v3.1 assembler. Corrected Illumina reads were used to correct the PacBio reads with LoRDEC v0.2. Illumina and PacBio reads were analyzed with SPAdes v3.1, which produced a raw draft assembly. Contigs from the draft assembly were merged into scaffolds with successive iterations of SSP […]

library_books

Genome re annotation of the wild strawberry Fragaria vesca using extensive Illumina and SMRT based RNA seq datasets

2017
PMCID: 5824900
PMID: 29036429
DOI: 10.1093/dnares/dsx038

[…] 3′ primer, and a poly-A tail were further selected for downstream analysis. Next, these full-length reads were collapsed into consensus transcripts by ICE and Quiver in the isoseq_cluster panel. The LoRDEC software was used to correct the sequencing errors in the consensus transcripts using Illumina reads as the reference (parameters: -k 19 -s 3). The corrected consensus transcripts were then map […]

library_books

Gaining comprehensive biological insight into the transcriptome by performing a broad spectrum RNA seq analysis

2017
Nat Commun
PMCID: 5498581
PMID: 28680106
DOI: 10.1038/s41467-017-00050-4

[…] rates including LSC, proovread, LoRDEC, and PBcR, . Here we analysed the hybrid long-read error correction tools LSC and LoRDEC.LSC was ~100× slower than LoRDEC (Supplementary Table ). Using LSC and LoRDEC on MCF7 data led to a 6.8% and 4.6% respective increase in the number of mapped reads compared to the raw long reads. However, reads corrected by LSC were of lower quality when compared to LoRD […]


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LoRDEC institution(s)
Department of Computer Science and Helsinki Institute for Information Technology HIIT, University of Helsinki, Finland; LIRMM and Institut de Biologie Computationelle, CNRS and Universite Montpellier, Montpellier, France
LoRDEC funding source(s)
Supported by Academy of Finland (267591), by ANR Colib’read (ANR-12-BS02-0008) and Defi MASTODONS SePhHaDe from CNRS, and Labex NumEV, as well as the ATGC platform.

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