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DBG2OLC specifications

Information


Unique identifier OMICS_13517
Name DBG2OLC
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Long reads from Illumina or PacBio, Consensus information, DBG contigs
Input format FASTQ, FASTA, TXT
Output data An overlap graph, the draft assembly
Biological technology Illumina, Pacific Biosciences
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Chengxi Ye <>

Publication for DBG2OLC

DBG2OLC in publications

 (13)
PMCID: 5920183
PMID: 29700132
DOI: 10.1128/genomeA.00122-18

[…] of 300 bp for illumina and 20 kb for pacbio were prepared using a nextera xt-library preparation kit and p6-p4 chemistry, respectively. all sequencing reads from both platforms were assembled using dbg2olc software to produce scaffolds (). the genome sequencing resulted in a total genome size of 79.24 mb with 55.9% gc content, 826× sequencing coverage, 495 scaffolds, n50 scaffold length […]

PMCID: 5836269
PMID: 29267857
DOI: 10.1093/gigascience/gix128

[…] 31 g 15 pathcovth 100 gs 1 800 000 000. next, (ii) the resulting contigs were assembled into scaffolds using pacific biosciences long subreads data and the pacbio-correction-free assembly algorithm dbg2olc [] with parameters ld1 0 k 17 kmercovth 10 minoverlap 20 adaptiveth 0.01. finally, (iii) resulting scaffolds were submitted to 6 iterative runs of the program l_rna_scaffolder [], which uses […]

PMCID: 5638244
PMID: 29023486
DOI: 10.1371/journal.pbio.2003790

[…] and p6 polymerase., in order to get the best assembly results, we tried short oligonucleotide analysis package de novo assembly tool (soapdenovo) [], de bruijn graph to overlap-layout-consensus (dbg2olc) (https://sourceforge.net/projects/dbg2olc/), falcon (https://github.com/pacificbiosciences/falcon), and smartdenovo (https://github.com/ruanjue/smartdenovo). the assembly result […]

PMCID: 5824816
PMID: 28985356
DOI: 10.1093/dnares/dsx036

[…] subsequently, platanus (ver. 1.2.4) was executed using the preprocessed paired-end reads to assemble contigs (, step 1), which were then used as anchors to connect the pacbio long reads on dbg2olc (commit id: 7f1712ae76b015b1f4efee81a5d4e1305701197a) (, step 2). contigs from the platanus assembly that were longer than 1 kb were used for the input of the dbg2olc hybrid assembly. note […]

PMCID: 5449645
PMID: 28431028
DOI: 10.1093/gigascience/gix028

[…] parameters “-m 500 -k 43 -s 5 -d 0.3 -u 0.15 -c 3,” resulting in two contig assemblies. the platanus-generated contigs, together with pacbio reads, were used to generate a third contig assembly by dbg2olc with default parameters []. the three different contig assemblies were merged together by minimus2 amos (v. 3.1.0) using default parameters []. to eliminate possible errors of the merged […]


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DBG2OLC institution(s)
Department of Computer Science, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA; Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Agricultural Genome Institute, Chinese Academy of Agricultural Sciences, Dapeng New District, Shenzhen, Guangdong, China
DBG2OLC funding source(s)
This research received funding from the following sources: National Science Foundation of China (Grants No. 61175071, 71473243), the Exceptional Scientists Program and Top Oversea Scholars Program of Yunnan Province, and Yunling Industrial Innovation Grant.

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