DALIGNER protocols

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DALIGNER specifications

Information


Unique identifier OMICS_08897
Name DALIGNER
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Pacific Biosciences, Oxford Nanopore
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Documentation


DALIGNER in pipelines

 (2)
2017
PMCID: 5416750
PMID: 28062856
DOI: 10.1093/nar/gkw1328

[…] as second step in the porefume pipeline. nanocorrect has been applied previously to increase the nanopore read accuracy from 80.5% to 95.9% (). the algorithm identifies overlapping reads using daligner () and calculates a consensus sequence, using partial-order alignment (poa) software (). two rounds of error correction where conducted by the porefume pipeline. finally, the error corrected […]

2017
PMCID: 5627904
PMID: 28977016
DOI: 10.1371/journal.pone.0184741

[…] analysis, we adapted a previously described pipeline that relies on using de novo assembly of minion reads []. loman’s method uses the overlapping regions which are detected between reads using daligner [], which are then corrected by a multiple-alignment process using partial order aligner []. the corrected reads are assembled using the celera assembler [], producing a de novo assembled […]


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DALIGNER in publications

 (5)
PMCID: 5676039
PMID: 29114024
DOI: 10.1128/mBio.01470-17

[…] score of <55,000). reverse-complementary artificial reads created by the random amplification were next filtered out (cutoff match length of ≥1,000 bp) after mapping them onto themselves using daligner (https://github.com/thegenemyers/daligner/) (v1.0 [options -a and -i]). the cleaned reads were assembled using the tool falcon () (v0.2 [options length cutoff=8000m […]

PMCID: 5627904
PMID: 28977016
DOI: 10.1371/journal.pone.0184741

[…] analysis, we adapted a previously described pipeline that relies on using de novo assembly of minion reads []. loman’s method uses the overlapping regions which are detected between reads using daligner [], which are then corrected by a multiple-alignment process using partial order aligner []. the corrected reads are assembled using the celera assembler [], producing a de novo assembled […]

PMCID: 5314710
PMID: 28209125
DOI: 10.1186/s12864-017-3550-8

[…] sequences were pulled out via the pacbio long read aligner (blasr []) using the bighead goby mitochondrial genome [] as query. local multiple alignments of the mitochondrial reads were computed with daligner []. from the resulting overlaps, five high quality reads were selected as template genomes for the error correction step. then, these were extended on both sites by the overhang sequence […]

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

[…] 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 originally developed for processing pacbio raw data to correct […]

PMCID: 5093776
PMID: 27646134
DOI: 10.1016/j.gpb.2016.05.004

[…] consensus generation, and finally contig base polishing using the event data. the fasta sequences for reads are extracted using poretools and converted to the format expected by alignment tool daligner . potential overlaps between the reads are detected from the daligner alignments. multiple alignments are computed using the partial-order alignment (poa) software , where data inputs […]


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