LoRDEC protocols

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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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Maintainer


  • person_outline LoRDEC Team <>

Additional information


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

Publication for Long Read DBG Error Correction

LoRDEC in pipelines

 (2)
2017
PMCID: 5550469
PMID: 28794490
DOI: 10.1038/s41598-017-08138-z

[…] were subjected to isoform-level clustering by iec algorithm and herein produced consensus sequences of isoform. finally, the isoform sequences were corrected in aid of illumina short reads using lordec tool v0.6 with -k 21, -s 3, and default setting for other parameters., the corrected isoform sequences were aligned against reference genome using gmap aligner v2016-08-24 with the parameters: […]

2016
PMCID: 4938638
PMID: 27172223
DOI: 10.1534/g3.116.030056

[…] the libraries as follows. in the case of illumina libraries, exact read duplicates were removed using the ’in silico normalization’ utility from trinity. for pacbio, reads were error-corrected using lordec v0.4.1 based on the two paired-end illumina libraries (table s1). kmers ranging from 19 to 36 were tested for error-correction. we made an effort to assemble intact pacbio reads following […]


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LoRDEC in publications

 (12)
PMCID: 5816337
PMID: 29483921
DOI: 10.3389/fpls.2018.00005

[…] 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 […]

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

[…] assembly.3. step 3: obtained by performing jelly implemented in pbsuite based on canu assembly.4. step 4: obtained by performing jelly based on the smrt sequencing data that had been corrected by lordec, and performing pilon improvement and tablet for manual correction.5. step 5: obtained by comparative analysis of step4 assembled results and canu assembly.6. athe genome sequence of p. […]

PMCID: 5793194
PMID: 29346292
DOI: 10.3390/genes9010043

[…] of iso-seq isoforms is also improved with hiseq short reads []. in this case, certain programs have recently been developed such as pacbiotoca (error correction via celera assembler) [], lsc [], lordec [], and proovread []. pacbio long reads for phage, prokaryotic, and eukaryotic genome sequencing are corrected to 99.9% accuracy by pacbiotoca []. the computation method of lsc applies […]

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

[…] 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 […]

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 […]


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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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