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DRISEE specifications

Information


Unique identifier OMICS_27702
Name DRISEE
Alternative name Duplicate Read Inferred Sequencing Error Estimation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA,FASTQ
Operating system Unix/Linux, Mac OS
Programming languages Perl, Python, R, Shell (Bash)
Computer skills Advanced
Version 1.5
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Kevin Keegan

Publication for Duplicate Read Inferred Sequencing Error Estimation

DRISEE citations

 (6)
call_split

Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems

2017
Sci Rep
PMCID: 5562921
PMID: 28821820
DOI: 10.1038/s41598-017-09254-6
call_split See protocol

[…] maximum difference of 10% and were then processed for quality control. Low-quality regions were trimmed off using SolexaQA, de-replicated, and analyzed the artificially duplicated reads (ADRs) using Duplicate Read Inferred Sequencing Error Estimation (DRISEE). The near-exact matches against model organisms including fly, mouse, cow and human were removed using Bowtie. Coding regions in DNA sequen […]

library_books

Co registered Geochemistry and Metatranscriptomics Reveal Unexpected Distributions of Microbial Activity within a Hydrothermal Vent Field

2017
Front Microbiol
PMCID: 5468400
PMID: 28659879
DOI: 10.3389/fmicb.2017.01042

[…] Sequence data from all 20 metatranscriptomic libraries were analyzed in MG-RAST (http://metagenomics.anl.gov/) using default quality control parameters at submission, with the exception of running Duplicate Read Inferred Sequencing Error Estimation (DRISEE), which is designed to remove artificial duplicate read sequences, but can inadvertently eliminate biologically-relevant sequences from Illu […]

call_split

Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps

2016
Sci Rep
PMCID: 4764845
PMID: 26905381
DOI: 10.1038/srep21631
call_split See protocol

[…] format of samples (the largest and the smallest) was uploaded to MG-RAST server version 3.5. For quality control, firstly, dereplication (removing artificial replicate sequences) was performed using DRISEE (duplicate read inferred sequencing error estimation). Secondly, the removal of low quality sequences was performed by a modified DynamicTrim. After filtering, data gene calling was performed u […]

call_split

Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary

2016
Front Microbiol
PMCID: 4726783
PMID: 26858690
DOI: 10.3389/fmicb.2015.01438
call_split See protocol

[…] a). Sequences were subsequently analyzed using the Meta Genome Rapid Annotation using Subsystems Technology (MG-RAST, version 3.5; Meyer et al., ; Glass et al., ). Quality control was performed using DRISEE (Duplicate Read Inferred Sequencing Error Estimation) (Keegan et al., ) to check for Artificial Duplicate Reads (ADRs), and estimating sequence error (Gomez-Alvarez et al., ) within the MG-RAST […]

library_books

Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations

2015
Front Bioeng Biotechnol
PMCID: 4585024
PMID: 26442255
DOI: 10.3389/fbioe.2015.00141

[…] (Johnson et al., ). Data generation was not straightforward since scripts required some changes in order to work properly.Error rate and quality error models were first generated using the algorithm “duplicate read inferred sequencing error estimation” (DRISEE) (Keegan et al., ) with real paired-end (2 bp × 300 bp) sequencing output (fastq) from an Illumina MiSeq from Nextera metagenomic libraries […]

library_books

Comparative Analysis of the Intestinal Bacterial and RNA Viral Communities from Sentinel Birds Placed on Selected Broiler Chicken Farms

2015
PLoS One
PMCID: 4311960
PMID: 25635690
DOI: 10.1371/journal.pone.0117210

[…] aw nucleotide sequence for each pooled contact bird metagenome was uploaded to the MG-RAST metagenomics analysis server [], and subjected to the stringent MG-RAST quality pipeline, which consisted of duplicate read inferred sequencing error estimation (DRISEE)—a method to estimate sequencing error that is independent of the high-throughput sequencing platform used []; a dereplication step to remov […]

Citations

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DRISEE institution(s)
Argonne National Laboratory, Argonne, IL, USA; University of Chicago, Chicago, IL, USA; Institute for Genomics and Systems Biology, Chicago, IL, USA
DRISEE funding source(s)
Supported by the U.S. Department of Energy, Office of Biological and Environmental Research under Contract DE-AC02-06CH11357 as part of the DOE Systems Biology Knowledgebase.

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