Ergatis protocols

View Ergatis computational protocol

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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

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Maintainer


  • person_outline Joshua Orvis <>

Publication for Ergatis

Ergatis in pipeline

2011
PMCID: 3111993
PMID: 21677861
DOI: 10.4056/sigs.1223234

[…] the pipeline uses open source or free software whenever possible. all unique tools written specifically for the pipeline are written in perl and distributed under the gnu public license on the ergatis sourceforge website., the pipeline starts by splitting the multi-sequence nucleotide fasta file into individual files. non-coding rna and protein coding genes are predicted first, in parallel […]


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Ergatis in publications

 (60)
PMCID: 5829826
PMID: 29487233
DOI: 10.1128/mBio.00097-18

[…] the libraries were sequenced as 150-bp reads on the illumina hiseq 4000., 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 […]

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

[…] sequencing at the institute for genome sciences genome resource center on an illumina hiseq platform., 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 […]

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

[…] rna-seq system (nugen), and sequenced using 100 bp paired-end sequencing on the illumina hiseq., 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 […]

PMCID: 5399271
PMID: 28428312
DOI: 10.1128/genomeA.00241-17

[…] into 1.5-kbp overlapping shreds (, ). all shreds were integrated using phrap (). ninety-four contigs with an average 310× genome coverage were obtained. the assembled data were annotated using an ergatis-based () workflow, with minor manual curation. the genome size was found to be 6,733,904 bp, comprising 6,195 protein-coding genes. p. fluorescens s613 is currently explored […]

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

[…] 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 […]


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

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