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Otupipe specifications

Information


Unique identifier OMICS_16931
Name Otupipe
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.1.9
Stability Stable
Source code URL http://drive5.com/otupipe/otupipe1.1.9.tz
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Robert Edgar

Otupipe citations

 (22)
call_split

Antibiotic‐mediated bacteriome depletion in ApcMin/+ mice is associated with reduction in mucus‐producing goblet cells and increased colorectal cancer progression

2018
PMCID: 5943478
PMID: 29624892
DOI: 10.1002/cam4.1460
call_split See protocol

[…] NA from fresh feces were isolated using the MoBio PowerSoil DNA Isolation Kit and subjected to 16S rRNA gene analysis . The 16S metadata were demultiplexed with QIIME , . OTUs were shortlisted using OTUPipe analysis pipeline for error correction, chimera checking, UCLAST clustering and picking the optimal representative sequence centroid. Reference‐based chimera checking was conducted against a s […]

call_split

Studies on bacterial community composition are affected by the time and storage method of the rumen content

2017
PLoS One
PMCID: 5409139
PMID: 28453579
DOI: 10.1371/journal.pone.0176701
call_split See protocol

[…] e reads OTUs with a 97% cutoff, and to assign the taxonomy using the Ribosomal Database Project (RDPII) version 10 []. Bacterial sequences were de-noised and suspected chimeras were removed using the OTUpipe function within QIIME. Sequence data were were summarized at the phylum, class, and family levels; in addition, Alpha_diversity.py in QIIME was used to calculate ACE, Chao1, Shannon and Simpso […]

library_books

Novel Rhizosphere Soil Alleles for the Enzyme 1 Aminocyclopropane 1 Carboxylate Deaminase Queried for Function with an In Vivo Competition Assay

2016
Appl Environ Microbiol
PMCID: 4751833
PMID: 26637602
DOI: 10.1128/AEM.03074-15

[…] ME software package (Quantitative Insights into Microbial Ecology), using the default parameters for each step (). The sequences were chimera checked and clustered into ACCD-DR variant clusters using OTUpipe () at 99% sequence identity. Each ACCD-DR variant cluster (equivalent to an operational taxonomic unit [OTU] in 16S rRNA analysis) was represented by its most abundant sequence. A total of 33, […]

library_books

Probiotic Bifidobacterium longum alters gut luminal metabolism through modification of the gut microbial community

2015
Sci Rep
PMCID: 4552000
PMID: 26315217
DOI: 10.1038/srep13548

[…] ing the fastq-join script in ea-utils (ver. 1.1.2–537). Potential chimeric sequences were removed by reference-based chimera checking in USEARCH (ver. 5.2.32) and the gold database (http://drive5.com/otupipe/gold.tz). The non-chimeric sequences were analyzed in the QIIME software package, version 1.7.0, using closed-reference operational taxonomic unit (OTU) picking against 16S rRNA genes of the 1 […]

call_split

High nutrient availability reduces the diversity and stability of the equine caecal microbiota

2015
PMCID: 4526772
PMID: 26246403
DOI: 10.3402/mehd.v26.27216
call_split See protocol

[…] ome Junior Sequencer system (Roche Diagnostics, Mannheim, Germany) by the microbial laboratory facility of Nofima (Ås, Norway).Filtering analysis of sequencing data on each sample was conducted using OTUpipe available at the homepage of QIIME. OTUpipe is a pipeline script built using USEARCH (high-throughput biological sequence analysis) (www.drive5.com/usearch/) to perform filtering of noisy sequ […]

call_split

High diversity of protistan plankton communities in remote high mountain lakes in the European Alps and the Himalayan mountains

2015
PMCID: 4399440
PMID: 25764458
DOI: 10.1093/femsec/fiv010
call_split See protocol

[…] us nucleotides and a minimum length of 300 bp were kept. The remaining sequences were then checked for chimeras and clustered at different threshold levels (90, 95, 96, 97, 98, 99 and 100%) using the OTUpipe script (Edgar et al., ) implemented in QIIME. The OTUpipe script was done with the following adjustments: -m usearch –l –reference_chimera_detection –j 1 –s 0.xx –word_length yy. The word leng […]

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