Ergatis statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Ergatis
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Tool usage distribution map

This map represents all the scientific publications referring to Ergatis per scientific context
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Popular tool citations

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Protocols

Ergatis specifications

Information


Unique identifier OMICS_01140
Name Ergatis
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Joshua Orvis

Publication for Ergatis

Ergatis citations

 (31)
call_split

Phosphotyrosine Mediated Regulation of Enterohemorrhagic Escherichia coli Virulence

2018
MBio
PMCID: 5829826
PMID: 29487233
DOI: 10.1128/mBio.00097-18
call_split See protocol

[…] The Illumina reads generated for each RNA sample were analyzed and compared by using an in-house Ergatis-based () RNA-Seq analysis pipeline as previously described (). The reads were trimmed for quality with the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). The reads were th […]

library_books

Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome

2017
Int J Genomics
PMCID: 5603330
PMID: 28951866
DOI: 10.1155/2017/8724304

[…] Assembled genomes were annotated using a modified version of the IGS Annotation Engine (released by the University of Maryland, Institute for Genome Sciences at the School of Medicine) on an Ergatis workflow manager. Annotated genomes are available in GenBank under accession numbers NSCV1-1154-74: NZ_CP010811.1 and NSCV2-10432-62: NZ_CP010812.1. Post assembly genome sequence analysis was […]

library_books

Transcriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence Inducing Conditions

2017
mSystems
PMCID: 5527300
DOI: 10.1128/mSystems.00024-17

[…] The Illumina reads generated for each RNA sample were analyzed and compared using an in-house Ergatis-based () RNA-Seq analysis pipeline as previously described (). Briefly, the RNA-Seq reads were aligned to the corresponding genome sequences using Bowtie (), and the number of reads that align […]

library_books

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli

2017
Sci Rep
PMCID: 5471185
PMID: 28615618
DOI: 10.1038/s41598-017-03489-z

[…] The Illumina reads generated for each RNA sample were analyzed and compared using an in-house Ergatis-based RNA-Seq analysis pipeline as previously described. The completed genome sequence and annotation that is publicly available for EPEC isolate E2348/69 was used for the RNA-Seq analysis of […]

library_books

CloVR Comparative: automated, cloud enabled comparative microbial genome sequence analysis pipeline

2017
BMC Genomics
PMCID: 5408420
PMID: 28449639
DOI: 10.1186/s12864-017-3717-3

[…] costs, several test datasets (Table ) were run and compared on local desktop computers and different EC2 instance types (Table ). Runtimes were determined based on processing times recorded with the Ergatis workflow system [] that is part of the CloVR framework and used for process management. With the exception of the analysis of 40 E. coli genomes, all runs finished in around 24 h (E. coli run: […]

library_books

Genome Sequences of Eight Bacterial Species Found in Coculture with the Haptophyte Chrysochromulina tobin

2016
Genome Announc
PMCID: 5095461
PMID: 27811091
DOI: 10.1128/genomeA.01162-16

[…] eMapper version 2.3.0 (https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Bridgemapper) and were corrected using Consed (). Annotations of corrected assemblies were completed using an Ergatis workflow with minor manual curation (). Bacterial taxonomic affinity was assessed by aligning PCR-recovered and genome-sequence-acquired 16S ribosomal DNA sequences using the SILVA Incremental […]


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Ergatis institution(s)
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA

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