SOAP2denovo2-Aureus
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2025-11-11T16:44:53.047+01:00
type: RoCrateNanopub

N003bb036f6b64fb6bee352161d423250
port name: KmerFreq AR/Library1/Reverse FASTQ file
resource: Inputs/saureus A L1 101bp180IS45X 2.fq
type: inputValue

N026919dbca3d46a4896c5b21dde7ca60
port name: SOAPdenovo2/Library2/Reverse FASTQ file
resource: Inputs/saureus B L3 37bp3500IS45X 2.fq
type: inputValue

N57bf95dede65492cb1fc4d613557e08d
port name: GAGE/Reference genome file in FASTA format
resource: Inputs/saureus.fasta
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Workflow input file for SOAPdenovo2
has artifact: Inputs/saureus B L3 37bp3500IS45X 1.fq
type: Input

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described by workflow: Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga
type: WorkflowRun

Workflow input file for SOAPdenovo2
has artifact: Inputs/saureus B L3 37bp3500IS45X 2.fq
type: Input
comment: TODO:Upload and share the data

Workflow input file for GAGE/Reference genome file in FASTA format
has artifact: Inputs/saureus.fasta
type: Input

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port name: KmerFreq AR/Library1/Forward FASTQ file
resource: Inputs/saureus A L1 101bp180IS45X 1.fq
type: inputValue

Workflow output file
has artifact: Outputs/gage.out.Tabular
type: Output

Workflow input file for KmerFreq AR
has artifact: Inputs/saureus A L1 101bp180IS45X 2.fq
type: Input

Workflow input file for KmerFreq AR
has artifact: Inputs/saureus A L1 101bp180IS45X 1.fq
type: Input

Nf6477456e35347bc95840236f6cd9150
port name: SOAPdenovo2/Library2/Forward FASTQ file
resource: Inputs/saureus B L3 37bp3500IS45X 1.fq
type: inputValue

S. Aureus
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mechanics
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assembly
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genome assembly
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genetics
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Application
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SOAP2denovo2-Aureus
author: Raul Palma
content size: 71593
creator: Raul Palma
date created: 2014-07-31 10:08:03.820000+00:00
date modified: 2025-10-18 11:54:52.614522+00:00
date published: 2014-07-31 10:08:03.820000+00:00
description: Application of SOAP2denovo2 to the S. Aureus genome assembly
encoding format: application/ld+json
license: no-permission
type: ResearchObject
type: LiveRO
type: Dataset
cite-as: Raul Palma. "SOAP2denovo2-Aureus." ROHub. Jul 31 ,2014. https://w3id.org/ro-id/2e023e94-f276-4281-8a0d-45568bb3755c.

Statements
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Workflows
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NanoStm
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Outputs
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sketch.png
author: Raul Palma
content size: 66514
creator: Raul Palma
date created: 2014-08-01 08:51:17.138000+00:00
date modified: 2022-03-25 16:46:54.443012+00:00
encoding format: image/png
license: no-permission
sd date published: 2014-08-01 08:51:17.138000+00:00
type: Sketch
type: Resource
type: MediaObject

Galaxy workflow for reproducing Table 2 of SOAPdenovo paper
input selected: http://w3id.org/isa/soapdenovo2/raw_data_file/17
input selected: http://w3id.org/isa/soapdenovo2/raw_data_file/18
input selected: http://w3id.org/isa/soapdenovo2/raw_data_file/19
input selected: http://w3id.org/isa/soapdenovo2/raw_data_file/21
input value: N003bb036f6b64fb6bee352161d423250
input value: N026919dbca3d46a4896c5b21dde7ca60
input value: N57bf95dede65492cb1fc4d613557e08d
input value: Nc52483b33082462d8ed7982e0ecf9b05
has input: Workflow input file for SOAPdenovo2
has input: Workflow input file for KmerFreq AR
has output: Workflow output file
has workflow definition: rluo2012-example-1-soapdenovo2-saureus
author: Raul Palma
content size: 15681
creator: Raul Palma
date created: 2014-07-31 10:09:34.217000+00:00
date modified: 2022-03-25 16:46:55.708205+00:00
description: Galaxy workflow for reproducing Table 2 of SOAPdenovo paper
license: no-permission
sd date published: 2014-07-31 10:09:34.217000+00:00
type: Resource
type: MediaObject
type: ComputationalWorkflow

Results calculating the N50 and corrected N50 scores
author: Raul Palma
content size: 31
creator: Raul Palma
date created: 2014-07-31 10:10:24.821000+00:00
date modified: 2022-03-25 16:46:57.542753+00:00
license: no-permission
sd date published: 2014-07-31 10:10:24.821000+00:00
type: Result
type: Resource
type: MediaObject
was generated by: Na127b693f85f46e3a8e09c3041419be9

genome assembly
type: Phrase
norm score: 99.6996996996997
score: 99.6

astronautics (general)
type: NASA
norm score: 100.0
score: 0.6523571610450745

astronautics
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norm score: 100.0
score: 0.6523571610450745

Application of SOAP2denovo2 to the S. Aureus genome assembly
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norm score: 94.6946946946947
score: 94.6

diligence
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norm score: 33.58348968105065
score: 17.9

earth sciences
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norm score: 100.0
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application
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norm score: 17.070484581497794
score: 15.5

genome
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norm score: 66.41651031894935
score: 35.4

genome
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norm score: 41.519823788546255
score: 37.7

Genetics
type: IPTC
path: Science and technology/Natural science/Biology/Genetics

S. Aureus
type: Lemma
norm score: 41.409691629955944
score: 37.6

application of SOAP2denovo2
type: Phrase
norm score: 0.3003003003003003
score: 0.3

oceanography
type: FieldOfResearch
norm score: 100.0
score: 0.7194013595581055

SOAP2denovo2-Aureus.
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norm score: 5.305305305305306
score: 5.3

Raul Palma
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service-account-enrichment
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service-account-generation-service
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sig
has algorithm: RSA
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