pbdagcon statistics

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Citations per year

Number of citations per year for the bioinformatics software tool pbdagcon

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This map represents all the scientific publications referring to pbdagcon per scientific context
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pbdagcon specifications


Unique identifier OMICS_18567
Name pbdagcon
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux
Programming languages C++, Python, Shell (Bash)
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Pacific Biosciences

pbdagcon citations


Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida

BMC Genomics
PMCID: 5490193
PMID: 28659179
DOI: 10.1186/s12864-017-3852-x

[…] Minimus2 []. The remaining two gaps were resolved by blasting the trimmed edges of the scaffolds to the PacBio library in search for reads bridging them. Consensuses of these reads were created with PBdagcon (https://github.com/PacificBiosciences/pbdagcon), after which they were manually inserted into the assembly. Thereafter all reads were mapped back to the assembly and a consensus was created […]


Genome sequencing and analysis of Talaromyces pinophilus provide insights into biotechnological applications

Sci Rep
PMCID: 5428652
PMID: 28352091
DOI: 10.1038/s41598-017-00567-0

[…] I, Shenzhen, China). Four SMRT cells zero-mode waveguide arrays of sequencing, were used by the PacBio platform to generate the subreads set. PacBio subreads (length < 1 kb) were removed. The program Pbdagcon (https://github.com/PacificBiosciences/pbdagcon) was used for self-correction. Draft genomic unitigs, which are uncontested groups of fragments, were assembled using the Celera Assembler agai […]


Single Molecule Sequencing of the Drosophila serrata Genome

PMCID: 5345708
PMID: 28143951
DOI: 10.1534/g3.116.037598
call_split See protocol

[…] within the Celera Assembler (version 8.3rc2) (), and polished with Quiver (GenomicConsensus version 0.9.2 and ConsensusCore version: 0.8.8) () in three steps: (1) errors were corrected in reads using PBDagCon, which requires at least 50 × genome coverage and utilizes the consensus of oversampled sequences (); (2) overlapping sequences were assembled using MHAP and the Celera Assembler (); and (3) […]


TP53 gene mutation analysis in chronic lymphocytic leukemia by nanopore MinION sequencing

Diagn Pathol
PMCID: 5057401
PMID: 27724982
DOI: 10.1186/s13000-016-0550-y

[…] strategies: the Nanocorrect correction pipeline, specific for Nanopore data [], and the more generic ALEC (Amplicon Long-read Error Correction) python script [].Nanocorrect is a pipeline inspired by pbdagcon (https://github.com/PacificBiosciences/pbdagcon) which uses DALIGNER (https://github.com/thegenemyers/DALIGNER) and poa [] to correct sequencing errors in Nanopore reads. ALEC script has been […]


INC Seq: accurate single molecule reads using nanopore sequencing

PMCID: 4970289
PMID: 27485345
DOI: 10.1186/s13742-016-0140-7

[…] uence, but we conservatively excluded this option. Median accuracy of INC-Seq reads was improved further (to >98 %) using alternate mappers (GraphMap) to align the segments and by iteratively running PBDAGCON to improve the consensus. In principle, with the use of six or more segment copies, INC-Seq consensus reads should be more accurate than observed, but this is likely to require the developmen […]


Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the Collembolan Orchesella cincta

Genome Biol Evol
PMCID: 4987106
PMID: 27289101
DOI: 10.1093/gbe/evw134

[…] elly v. 2.2.0 (). Finally, we used HaploMerger (release: 20120810) () to discard all duplicate heterozygous contigs and to define the reference haploid assembly. The final polishing was done with the Pbdagcon (c = 2, m = 200) () and with the Pilon software (–fix bases, –diploid) (). Finally, we used VecScreen against the UniVec database to remove the remaining vector contamination. The completenes […]

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