DeconSeq protocols

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DeconSeq specifications

Information


Unique identifier OMICS_01418
Name DeconSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for DeconSeq

DeconSeq in pipelines

 (23)
2018
PMCID: 5819196
PMID: 29458340
DOI: 10.1186/s12866-018-1154-3

[…] qiime, concatenation of the data from all four sequencing runs and dereplication (collapsing into unique sequences) with usearch. reads that aligned to the human genome (grch38_p2) were removed with deconseq v0.4.3 [] using identity threshold 94% and coverage threshold 90%. remaining reads were clustered into otus (operational taxonomic units) at a 97% identity threshold with usearch to create […]

2018
PMCID: 5864009
PMID: 29566006
DOI: 10.1371/journal.pone.0194366

[…] ion torrent dataset was first preprocessed to remove duplicates and sequences of low quality (minimum quality score of 18), followed by further screening and removal of human-derived sequences using deconseq version 0.4.3, removing reads with a minimum overlap of 95% and >94% similarity to the human reference sequences. the corresponding ion torrent data are available on the sra ncbi archive […]

2017
PMCID: 5241873
PMID: 28098253
DOI: 10.1038/srep40920

[…] read merger (pear) software was used to merge and extend the paired-end illumina reads using the default parameters. the extended reads were analyzed against the human genome database using the deconseq program, with an identity and coverage cutoff of 70%, to remove human rna sequences. non-human reads were analyzed against all genbank viral genomes (65 052 sequences) using the blast […]

2017
PMCID: 5310281
PMID: 28198672
DOI: 10.1186/s12864-016-3254-5

[…] score lower than 15, or with a read length out of the range of 3σ from the mean read length, or with more than 1% missing base pairs (bp), were filtered out. duplicate sequences were also removed. deconseq [] was next used to remove contaminated reads originating from the human genome, i.e., those reads mapped to the human genome with over 98% identity and over 98% base pairs aligned. finally, […]

2017
PMCID: 5310281
PMID: 28198672
DOI: 10.1186/s12864-016-3254-5

[…] can be stable, progressing or unknown., we constructed a bioinformatics pipeline (fig. ) consisting of six steps, as follows: (1) quality control and preprocessing, in which tagcleaner, prinseq, deconseq and flash [–] were used to remove low quality reads and contamination from the human genome; (2) expanded phylogenetic analysis, in which metaphlan [] was used to sensitively detect […]


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DeconSeq in publications

 (84)
PMCID: 5942804
PMID: 29742151
DOI: 10.1371/journal.pone.0197053

[…] under bioproject prjna215355 (listeria monocytogenes database, us food and drug administration genometrakr project) (). sequencing contaminants were trimmed and removed using trimmomatic and deconseq [, ]. the l. monocytogenes genomes were assembled using spades v. 3.8.0 []. contigs < 500 bp were trimmed from each genome file. st, cc, deduced serogroups, and lineage assignments […]

PMCID: 5902848
PMID: 29661147
DOI: 10.1186/s12864-018-4658-1

[…] with some host dna, the amount of host contamination was determined and removed by alignment against the b. rapa (assembly gca_000309985.1) and b. napus (assembly gca_000686985.1) genomes using deconseq 0.4.3 []. the demultiplexed reads were aligned to the p. brassicae genome (assembly gca_001049375.1) using mosaik 2.2.3 []. variant calling was performed using freebayes v0.9.21 []. […]

PMCID: 5901865
PMID: 29661185
DOI: 10.1186/s12915-018-0509-4

[…] reads. scaffolds shorter than 500 bp were discarded from the genome assembly. resultant scaffold sequences were further screened for contaminated organismal and artificial sequences employing deconseq v0.4.3 [] (additional file : supplementary methods; additional file : figure s17)., the n50 scaffold lengths of the genome assemblies of p. picta and other reptiles were computed using […]

PMCID: 5928460
PMID: 29617986
DOI: 10.1093/femsle/fny082

[…] was done using interactive tree of life (itol) (letunic and bork )., quality control and filtering of transcriptome data were performed with trimmomatic, pear (paired-end read merger) and deconseq. trimmomatic trimmed adapter sequences, low-quality reads and removed ns (bolger, lohse and usadel ). pear combined overlapping paired reads into a single read (zhang et al.). deconseq […]

PMCID: 5819196
PMID: 29458340
DOI: 10.1186/s12866-018-1154-3

[…] qiime, concatenation of the data from all four sequencing runs and dereplication (collapsing into unique sequences) with usearch. reads that aligned to the human genome (grch38_p2) were removed with deconseq v0.4.3 [] using identity threshold 94% and coverage threshold 90%. remaining reads were clustered into otus (operational taxonomic units) at a 97% identity threshold with usearch to create […]


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DeconSeq institution(s)
Department of Computer Science, San Diego State University, San Diego, CA, USA

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