pbdagcon statistics

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pbdagcon specifications

Information


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

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  • person_outline Pacific Biosciences <>

pbdagcon in publications

 (6)
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] sets using pacbio’s hgap error correction [] and filtering with a minimum read quality of 0.75, minimum subread length of 500 bp and coverage cutoff of 30× (https://github.com/pacificbiosciences/pbdagcon). alignments were performed using blasr version (1.3.1.142244) [] with minimum read length of 200 bp and reads skipped that had a length less than a maximum score of − 1000 across their full […]

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

[…] 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 […]

PMCID: 5345708
PMID: 28143951
DOI: 10.1534/g3.116.037598

[…] we generated 12 gbp of raw sequence data comprising ∼65 × whole-genome coverage. read lengths averaged 8940 bp (nread50 12,200) with the longest read at 53 kbp. we self-corrected reads using the pbdagcon algorithm and assembled the genome using the mhap algorithm within the pbcr assembler. total genome length was 198 mbp with an n50 just under 1 mbp. contigs displayed a high degree […]

PMCID: 5416750
PMID: 28062856
DOI: 10.1093/nar/gkw1328

[…] score of 15 was used in both cells. the extracted reads of insert were grouped by individual barcode and exported in the fastq. the final yield is reported in ., pacbio reads were collapsed with pbdagcon (https://github.com/pacificbiosciences/pbdagcon, version f19aed1) using dazcon with the flags –only-proper-overlaps and –coverage-sort and parameter –min-coverage 0., the integron structure […]

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

[…] 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 […]


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