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COPE specifications

Information


Unique identifier OMICS_05256
Name COPE
Alternative name Connecting Overlapped Pair-End
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for Connecting Overlapped Pair-End

COPE citations

 (5)
call_split

Shifts in Host Mucosal Innate Immune Function Are Associated with Ruminal Microbial Succession in Supplemental Feeding and Grazing Goats at Different Ages

2017
Front Microbiol
PMCID: 5582421
PMID: 28912767
DOI: 10.3389/fmicb.2017.01655
call_split See protocol

[…] Microbial Ecology (QIIME) () and Mothur (). Reads were deconvoluted into individual samples based on their barcodes. The pair-end reads were assembled based on their overlapped sequences using COPE (Connecting Overlapped Pair-End) () and trimmed of primers.For bacteria and archaea, the assembled sequences were assigned to operational taxonomic units (OTUs) at a 97% identity threshold using UPARSE […]

call_split

High Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation

2016
PLoS One
PMCID: 5167551
PMID: 27992473
DOI: 10.1371/journal.pone.0168166
call_split See protocol

[…] than one ambiguous base (N); (2) confirmation of barcode and adaptor completeness; (3) removal of sequences shorter than 100 bp. All 250 bp pair-end sequence reads were connected using COPE software (Connecting Overlapped Pair-end, V 1.2.1) [] to merge read pairs into tags from DNA fragments. Further data processing was performed as previously described [–,] and included removal of sequencing nois […]

call_split

Association between gut microbiota and diapause preparation in the cabbage beetle: a new perspective for studying insect diapause

2016
Sci Rep
PMCID: 5146961
PMID: 27934967
DOI: 10.1038/srep38900
call_split See protocol

[…] Based on the raw data (The Sequence Read Archive accession: SRP078307), pair-end reads were spliced using the principle of 98% overlap of 19 bases using Connecting Overlapped Pair-End software. Barcode and primer sequences were then filtered to obtain clean data. Operational Taxonomic Unit (OTU) generation and clustering were done with USEARCH on the […]

call_split

Gradual Changes of Gut Microbiota in Weaned Miniature Piglets

2016
Front Microbiol
PMCID: 5090779
PMID: 27853453
DOI: 10.3389/fmicb.2016.01727
call_split See protocol

[…] , and its paired reads were removed; (4) those reads with low complexity (default: reads with 10 consecutive same base) were removed. The paired-end clean reads with overlap were merged to tags using Connecting Overlapped Pair-End (COPE, V1.2.1) (Liu et al., ) software. Subsequently, bacterial tags were clustered into Operational Taxonomic Units (OTUs) at 97% sequence similarity by scripts of Moth […]

call_split

Composition of Ileal Bacterial Community in Grazing Goats Varies across Non rumination, Transition and Rumination Stages of Life

2016
Front Microbiol
PMCID: 5011132
PMID: 27656165
DOI: 10.3389/fmicb.2016.01364
call_split See protocol

[…] 16S rRNA reads were analyzed using QIIME () and mothur () pipeline. Pair-end reads were deconvoluted into individual samples based on their barcodes and assembled base on their overlap sequence using Connecting Overlapped Pair-End (COPE; ). After primer trimming, the assembled sequences were then assigned to operational taxonomic units (OTUs) at 97% similarity using UPASE (). Sequence alignment wa […]

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COPE institution(s)
HKU-BGI BAL-Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong

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