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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 citations

 (6)
library_books

Mechanisms of Surface Antigenic Variation in the Human Pathogenic Fungus Pneumocystis jirovecii

2017
MBio
PMCID: 5676039
PMID: 29114024
DOI: 10.1128/mBio.01470-17

[…] rected 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 and length_cutoff_pr=1000] […]

library_books

The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish

2017
BMC Genomics
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 of o […]

library_books

Rapid resistome mapping using nanopore sequencing

2017
Nucleic Acids Res
PMCID: 5416750
PMID: 28062856
DOI: 10.1093/nar/gkw1328

[…] mented 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 […]

library_books

Innovations and challenges in detecting long read overlaps: an evaluation of the state of the art

2016
Bioinformatics
PMCID: 5408847
PMID: 28003261
DOI: 10.1093/bioinformatics/btw811

[…] as the min-k-mer can degrade the performance of overlap detection. To minimize the effect of repetitive elements, Minimap uses an invertible hash function when choosing min-k-mers. This is similar to DALIGNER’s use of DUST; it works by preventing certain hash values that correspond to low complexity sequences. Similar to DALIGNER, Minimap automatically splits datasets into batches (blocks) to redu […]

library_books

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

2016
Diagn Pathol
PMCID: 5057401
PMID: 27724982
DOI: 10.1186/s13000-016-0550-y

[…] re 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 rando […]

library_books

Oxford Nanopore MinION Sequencing and Genome Assembly

2016
PMCID: 5093776
PMID: 27646134
DOI: 10.1016/j.gpb.2016.05.004

[…] tion, 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 are sin […]

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