DeconSeq protocols

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

 (7)
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: 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 [24] 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. […]

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

[…] can be stable, progressing or unknown., we constructed a bioinformatics pipeline (fig. 1) consisting of six steps, as follows: (1) quality control and preprocessing, in which tagcleaner, prinseq, deconseq and flash [22–25] were used to remove low quality reads and contamination from the human genome; (2) expanded phylogenetic analysis, in which metaphlan [26] was used to sensitively detect […]

2016
PMCID: 5010895
PMID: 27412606
DOI: 10.1093/gbe/evw158

[…] data following the same protocol as for the two asymmetron libraries: raw reads were processed by trimmomatic (v0.32) (bolger et al. 2014), prinseq (v0.20.4) (schmieder and edwards 2011b), and deconseq (v0.4.3) (schmieder and edwards 2011a) sequentially to trim the sequence and remove potential contamination; trinity (r20131110) (grabherr et al. 2011) and transdecoder […]

2015
PMCID: 4428251
PMID: 25969736
DOI: 10.1186/s40168-015-0083-8

[…] arising from the high levels of non-bacterial dna in the adenoid biopsies. we note there are a variety of stand-alone methods available to eliminate this type of non-bacterial signal, such as deconseq [12], kraken [11] and fastq screen (babraham bioinformatics, babraham institute, uk). however, by utilising parameters in qiime, we were able to achieve an efficient removal […]

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

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