Collection of datasets containing the TaxaSE bacterial taxonomic annotation pipeline, SILVA insilico datasets and Illumina sequencing data from sugarcane bacterial (16S) including subhabitats from soil, rhizosphere, stem and root

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Title
Collection of datasets containing the TaxaSE bacterial taxonomic annotation pipeline, SILVA insilico datasets and Illumina sequencing data from sugarcane bacterial (16S) including subhabitats from soil, rhizosphere, stem and root
Type
Dataset
Date Record Created
2017-05-17
Date Record Modified
Not provided
Language
English
Embargo
Embargo
Not embargoed.
Embargo date
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Embargo comment
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Coverage
Date Coverage
2013-02-01 to 2017-02-28
Time Period
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Geospatial Location
Not provided
Description
  1. This dataset contains the TaxaSE bacterial taxonomic annotation pipeline (including its source code and associated data files). Insilico data generated from SILVA Release 123 database is also provided here, consisting of both whole SILVA and Removal of Taxa based validation approaches, which were used to compare Shannon entropy based sequence similarity approach to Percentage Identity (via USEARCH v7.0.1090 32bit, see Edgar 2010). Lastly, the raw FASTQ files as well as processed FASTA files from Sugarcane (Saccharum Spp.) are included, consisting of samples from soil, rhizosphere, root and stem sub-habitats, alongside results generated in QIIME 1.9.1 (Caporaso et.al 2010).

    The quality of all Illumina R1 and R2 reads were assessed visually using FASTQC (Andrews 2016), merged using FLASH (Magoč & Salzberg 2011) and converted to FASTA format using QIIME’s “convert_fastaqual_fastq.py” script. Alpha diversity and beta diversity analysis were performed in QIIME, with TaxaSE results converted to QIIME compatible format for comparison. Insilico data was generated using MicroSim simulator from SILVA 123 Release database. Sugarcane leaf, stalk, root and rhizosphere soil samples were collected by Dr. Kelly Hamonts at Hawkesbury Institute for the Environment, Western Sydney University, Australia, in November 2014 from eight sugarcane fields growing three sugarcane varieties (KQ228, MQ239 and Q240) near Ingham, Queensland, Australia.

    In each field, 3 stools were randomly selected and samples were collected from 2 plants per stool. Samples were snap-frozen in liquid nitrogen on the field, transported to the laboratory on dry ice and stored at -80C. Frozen sugarcane tissue samples were ground using mortar and pestle and DNA was extracted from the resulting powder using the MoBio PowerPlant DNA extraction kit, following the manufacturer’s instructions. The MoBIO PowerSoil DNA extraction kit was used to extract DNA from the soil samples. Bacterial 16S rRNA amplicon sequencing was performed by the NGS facility at Western Sydney University using Illumina Miseq (2x 301 bp PE) and the 341F/805R primer set.

    • Type: full
Related Publications
  1. Ijaz, AZ, Jeffries, T, Quince, C, Hamonts K & Singh, B 2017, ‘TaxaSE: Exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation’, Peer J Preprints. DOI: 10.7287/peerj.preprints.2941v1
    Pre print
  2. Edgar, RC 2010, 'Search and clustering orders of magnitude faster than BLAST', Bioinformatics,vol. 26, no. 19, pp. 2460-2461.
    As mentioned in Description
  3. Caporaso, JG, Kuczynski, J, Stombaugh, J, Bittinger, K, Bushman, FD, Costello, EK et al. 2010, 'QIIME allows analysis of high-throughput community sequencing data', Nature Methods, vol. 7, no. 5, pp. 335-336.
    As mentioned in Description
  4. Magoč, T. & Salzberg, S 2011, ‘FLASH: Fast length adjustment of short reads to improve genome assemblies’, Bioinformatics, vol. 27, no. 21, pp. 2957-63.
    As mentioned in Description
Related Websites
  1. HIE | Hawkesbury Institute for the Environment
  2. A quality control tool for high throughput sequence data (Andrews S. 2016)
    As mentioned in Description
Related Data
Not provided
Related Services
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Technical metadata
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People
Creators
  1. Mr Ali Ijaz , Hawkesbury Institute for the Environment (HIE) [CI]
  2. Dr Kelly Hamonts , Hawkesbury Institute for the Environment (HIE)
  3. Dr Thomas Jeffries , Hawkesbury Institute for the Environment (HIE)
Primary Contact
Ali Ijaz, Ali.Ijaz@westernsydney.edu.au
Supervisors
Not provided
Subject
Fields of Research
  1. 060102 - Bioinformatics (060102)
  2. 080301 - Bioinformatics Software (080301)
  3. 060504 - Microbial Ecology (060504)
Socio-Economic Objective
Not provided
Keywords
  1. NGS
  2. Illumina
  3. Taxonomy
  4. Annotation
  5. Pipeline
  6. Community analysis
  7. SILVA
  8. Saccharum Spp
Research Activity
Pure basic research
Rights
License
CC BY 4.0: Attribution 4.0 International
License - Other
Not provided
Access Rights/Conditions
Check with the primary contact to negotiate access to the data
Type
open
Rights
Not provided
Attachments
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Citation
Sending Citation
on
Identifier Type
useCuration
Creators
  1. Mr Ali Ijaz
  2. Dr Kelly Hamonts
  3. Dr Thomas Jeffries
Title
Collection of datasets containing the TaxaSE bacterial taxonomic annotation pipeline, SILVA insilico datasets and Illumina sequencing data from sugarcane bacterial (16S) including subhabitats from soil, rhizosphere, stem and root
Edition
Not provided
Publisher
Western Sydney University
Place of Publication
Not provided
Dates
  1. 2017-05-17 {missing: "dc:type.skos:prefLabel" }
  2. 2017-05-17 Date Created
URL
http://doi.org/10.4225/35/591bd33340e36
Context
Ijaz, Ali; Hamonts, Kelly; Jeffries, Thomas (2017): Collection of datasets containing the TaxaSE bacterial taxonomic annotation pipeline, SILVA insilico datasets and Illumina sequencing data from sugarcane bacterial (16S) including subhabitats from soil, rhizosphere, stem and root. Western Sydney University. http://doi.org/10.4225/35/591bd33340e36