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Recycler specifications

Information


Unique identifier OMICS_11194
Name Recycler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
Numpy, Networkx, PySAM, nose
Maintained Yes

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Documentation


Maintainer


  • person_outline Eran Halperinr

Publication for Recycler

Recycler citations

 (10)
library_books

Draft Genome Sequences of Four Clinical Legionella pneumophila Isolates from Ontario, Canada

2018
Genome Announc
PMCID: 5897800
PMID: 29650583
DOI: 10.1128/genomeA.00295-18

[…] Ades () to identify potential plasmids. We identified a plasmid contig in the LG57 strain. For confirmation, a BAM file including all paired-end reads and the SPAdes assembly graphs were submitted to Recycler (), confirming a 76,262-bp plasmid with high sequence similarity (97%) to a 31.9-kb fragment of the L. pneumophila subsp. pneumophila strain Lorraine plasmid pLELO (GenBank accession no. FQ95 […]

library_books

PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data

2018
Microb Genom
PMCID: 5885016
PMID: 29533742
DOI: 10.1099/mgen.0.000164

[…] that can combine short- and long-read data to produce fully circularized chromosomes and plasmids. It essentially fixes many of the deficiencies of SPAdes[] and fine-tunes it for assembling bacteria. Recycler [] takes an assembly graph and aligned reads to search for cycles in the graph that may correspond to plasmids. The method is only partially implemented, with substantial work required on the […]

library_books

Systematic Review: Occupational illness in the waste and recycling sector

2017
PMCID: 5927023
PMID: 29165683
DOI: 10.1093/occmed/kqx153

[…] ung function in children and neonatal defects including stillbirths, premature births and low birth weights in China []. There was one case report from the USA of argyria in an X-ray and photographic recycler [].HSE’s Reporting of Injuries, Diseases and Dangerous Occurrences Regulations (RIDDOR) identified four cases of occupational asthma, two of Q fever, two of leptospirosis, one of extrinsic al […]

library_books

Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa

2017
BMC Genomics
PMCID: 5681832
PMID: 29126393
DOI: 10.1186/s12864-017-4216-2

[…] s like genome coverage, read length and presence of repetitive sequences on the plasmid []. Due to these limitations, we applied three different bioinformatics tools (PlasmidFinder, plasmidSPAdes and recycler) to our dataset in order to augment plasmid detection [–]. Furthermore, plasmids predicted using these tools were only interpreted in combination with a manual search for annotated plasmid-sp […]

library_books

On the (im)possibility of reconstructing plasmids from whole genome short read sequencing data

2017
Microb Genom
PMCID: 5695206
PMID: 29177087
DOI: 10.1099/mgen.0.000128

[…] ds for plasmid prediction, we excluded PLACNET from the comparison.More recently, two algorithms that predict plasmids on the basis of the information contained in the de Bruijn graph were published: Recycler [] and PlasmidSPAdes []. Recycler extracts the information from the de Bruijn graph searching for sub-graphs (cycles) corresponding to plasmids. Selection of the cycles is based on the follow […]

library_books

The Cyanobacteria Dominated Sponge Dactylospongia elegans in the South China Sea: Prokaryotic Community and Metagenomic Insights

2017
Front Microbiol
PMCID: 5524777
PMID: 28790992
DOI: 10.3389/fmicb.2017.01387

[…] symbionts, but no genes associated with carbon fixation were found, which supported its heterotrophic lifestyle. There is a possibility that the Chloroflexi symbiont is a complementary scavenger and recycler of carbon compounds originating from seawater and the sponge host in addition to Poribacteria (Kamke et al., ).Besides the above sponge symbionts, Acidobacteria was also highly abundant in th […]

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Recycler institution(s)
Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv, Israel; Molecular Microbiology and Biotechnology Department, Tel-Aviv University, Tel Aviv, Israel; International Computer Science Institute, Berkeley, CA, USA; The Department of Life Sciences & the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel

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