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== MiSeq PE and Mitochrondrial reads ==
== HiSeq PE Data ==
= Mitochondrial genome =
... more- A_hancockii_mito_complete.fa (complete mitochrondrial genome)
= Nuclear genome =
- FRR3425_A_hancockii_noMITO_min_200.fasta (contigs > 200bp)
- FRR3425_A_hancockii_noMITO_belowCutoff_200.fasta (contigs < 200bp)
**Gene Calls (AUGUSTUS)**
- FRR3425.outfile (GFF)
- FRR3425.outfile.aa (Amino acid calls for genes)
- FRR3425.outfile.cdexons (Exons)
- FRR3425.outfile.codingseq (Coding seqs)
Legacy data - Fungal genomics - Published 07 Mar 2017
A collection of raw and analysed sequence resources across several Hieracium species and genotypes related to the study of apomixis. This collection was generated by the Asexual Seed Formation researc... moreh team in CSIRO led by Anna Koltunow.
This data collection supports the publication : Generation of an integrated Hieracium genomic and transcriptome resource enables exploration of small RNA pathways during apomixis initiation
David S. Rabiger, Jennifer M. Taylor, Andrew Spriggs, Melanie L. Hand, Steven T. Henderson, Susan D. Johnson, Karsten Oelkers1, Maria Hrmova, Keisuke Saito, Go Suzuki, Yasuhiko Mukai, Bernard J. Carroll and Anna M.G. Koltunow*
BMC Biology 2016
OCE, PDF, KOL014-RAB018, Switching betwe - Development and Characterisation of Hieracium Genomics Resource - Published 28 Apr 2017
Sphingobium yanoikuyae strain_B2_R1_001.fastq.gz
Sphingobium yanoikuyae strain_B2_R2_001.fastq.gz
*Velvet assembly as scaffolds or contigs*
*Annotation files - based on scaffolds*
Annotation Sphingobium yanoikuyae strain B2.faa
Annotation Sphingobium yanoikuyae strain B2.gff
*Putative cytochrome sequences*
*Putative plasmid sequence*
Sphingobium yanoikuyae strain B2 putative plasmid.zip - file contains the fasta, gene calls and BLAST matches for this contigless
Industrial Biotechnology - Stratetic Pro - Bacterial genomics - Published 19 Jul 2016
An increased number of genomes are being made public but few individual research are willing to take ownership of their own data. Indeed, the current model is for genome sequences to be handled by seq... moreuencing centers or large bioinformatic repositories (RefSeq or Ensembl). Even though using these widely used and standardized repositories and center is an excellent model to decrease the cost of completing a genome project, this comes at a cost. First, these groups have in-house pipelines built and customized for the projects that financially support them (i.e. small genomes of microbial human pathogens and largely fully complete genomes such as Drosophila or human) rather than say a highly polymorphic species from a natural ecosystem. Second, the lack of a robust funding model means that these repositories are do not have the resources to offer community-wide support and customization of a pipeline. Third, and perhaps most importantly, these centers and repositories usually lack the domain expertise associated with the biology of the species.
For these (and perhaps others?) reasons, genome consortia that have access to genomicists (or PhD students and post-docs willing to learn) are either collaborating with bioinformatic laboratories or investing in their own annotation capability. This endeveavour has been greatly helped by the public availability of the tools used by the repositories and sequencing centers (e.g. GMOD, Ensembl and sequencing-center specific platforms such as those from the Broad Institute). The GMOD project specifically specializes in compact, user friendly solutions that just_work. For example, MAKER requires a few minutes of configuration to deliver a standardized annotation for gene models. At the other side of the spectrum, Ensembl delivers a comprehensive solution, database and informatic pipelines that - in the hands of a highly-trained bioinformatician - can deliver the same depth and level of annotation as that used by the EBI. There really is no a solution that fits in-between. There is also almost no software that also wishes to educate the user rather than offering a black box. Finally, there is no solution that we know of that can also functionally annotate the genome (a la BLAST2GO but free) and then link the concept of gene model (feature) annotation with functional annotation.
The JAMg software was created to address the issue of creating gene models (feature annotation) and was built by Alexie Papanicolaou at the Commonwealth Scientific and Industrial Research Organisation (CSIRO) with some brilliant support from Brian Haas at the Broad Institute. The software and manual are written so that to guide the annotation process so that users can follow the process closely. Even though with JAMg you will not need another genome annotation pipeline, JAMg does not aim to replace other genome annotation pipelines (e.g. each sequencing center has its own): it does aim to support nascent genome annotators and (ultimately) educate its users about genome annotation in general. As part of our Just_Annotate series, JAMg links with JAMp and WebApollo to provide a first solution for users wishing to go from genome assembly to deriving biological hypotheses.
This BZ2-compressed tar archive provides the software, HTML documentation and licensing statements. The expanded folder tree requires at least 2.5 GB of disk space. JAMg software is written in Perl and is supported for Linux 64-bit computers. See the homepage at http://jamg.sourceforge.net for new versions.
Cont to TCP01 Dissecting Adaptive - genome annotation software development - Published 06 Jan 2015
Genomic information for Bacillus pumilus 'Fairview' including: all contigs Velvet split by base pair size.
1218.1 MECSM Phase 2 - Survey of microbiology in coal seam gas reservoirs - Published 10 Mar 2014
Genomic information for Cairneyella variabilis including:
- All protein calls from AUGUSTUS 2.6.1 (generated 24-10-2013)
- cdsexons calls from AUGUSTUS 2.6.1 (generated 24-10-2013)
- coding sequence ... morecalls for proteins from AUGUSTUS 2.6.1 (generated 24-10-2013)
- all contigs less than 1000 bp from Velvet
- all proteins with signal peptides from SignalP
- mitochondrial genome
Legacy data - Fungal genomics - Published 18 Sep 2014
The collection contains the genome sequence of a diverse collection of sheep. For each animal, sequence reads are available to a depth of approximately 10 fold genome coverage. Sequence reads are made... more available in BAM format. Sequence polymorphisms are made available in VCF format following comparison of each animal’s sequence to the sheep reference genome assembly (v3.1). To assist users with interpretation of the collection, the reference genome (FA format) and genome feature files (GFF3 format) are included for viewing using software such as the Integrative Genome Viewer (IGV).less
CLSD 1206.1 NextGenBreedOpt C2012/5905 - Genome sequencing - Published 22 Jul 2013
Example input files suitable for analysis by Eagle. The data were obtained from a large genome-wide association study (GWAS) performed in outbred mice and published on the Heterogeneous Stock Mouse we... moreb site. The data were reorganized to make it suitable for input into Eagle.
Acquired - Mouse Genome-wide Association Study Data - Published 24 May 2017
DNA samples from sheep from all over the world representing 3,500 samples from 90 breeds. This collection is held on behalf of the International Sheep Genomics Consortium (ISCG).
Legacy data - Biological Specimen Collections - Published 19 Nov 2012
454 16S and 18S amplicon data associated with the manuscript "Comparison of biofilm ecology supporting growth of individual Naegleria species in a drinking water distribution system."
1006.12 74718 Biofilm, Naegleria and amo - Aquatic Ecology Ecogenomics - Published 30 Jan 2017
Whether working on a model or non-model species for biomedical, economical or evolutionary research, next-generation sequencing has enabled biologists to rapidly generate a reference sequence for down... morestream applications and hypotheses generation. With the exception of a limited number of species, functional annotation is conducted by in-silico experiments based on sequence similarity. Some groups are also enriching their data with expression studies. JAMp is a platform that allows biologists to reclaim the analysis of transcript reconstruction experiments by providing an automated process for generating functional annotations and a user-friendly overview of these in-silico experiments. The entire software is built so that novice command-line users can take a transcriptome assembly and generate websites like those found in our demo.
This our GeoGenetics prototype on phylogeography and genetics to use a large array of data. Using Chado (GMOD.org) and web-services we have built most of the tool allowing for an interaction of geo-lo... morecated samples with an unlimited array of data types. The data can be hosted locally or from any other server that serves the GeoJSON format.
An added capability is the intersection of these data with more than 200 environmental layers derived from the Atlas of Living Australia.
A further prototype capability is the ability to search for RNAi matches, as developed for a USDA proposal called "Reducing off-target effects of RNAi pesticides via functional genomics".
Cont to TCP01 Dissecting Adaptive - GeoGenetics software development - Published 06 Jan 2015
A collection of DNA and deduced protein sequences corresponding to the protein-coding transcriptome of adult specimens of the freshwater atyid shrimp Paratya australiensis. The sequences are derived f... morerom specimens from a laboratory-based experiment involving the exposure of shrimp to drain water from a site affected by acidification due to oxidation and re-wetting of acid sulphate soils. Please see associated publication in BMC Genomics (Bain et al., De novo assembly and analysis of changes in the protein-coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water, BMC Genomics, accepted manuscript).less
CLSDApprop -Ecotoxi Risk/C2012/7814 - RNA-Seq and transcriptome assembly of Paratya australiensis exposed to acid sulfate drainage water - Published 17 Oct 2016
Supplementary data for the BMC Genomics paper titled: "Chemosensory genes identified in the antennal transcriptome of the blowfly Calliphora stygia"
1023.1 FF Cybernose - strategic - Calliphora stygia transcriptome - Published 11 Mar 2015
Supplementary data for the BMC Genomics paper titled: "Identification and Characterization of Three Chemosensory Receptor Families in the Cotton Bollworm Helicoverpa armigera"
Catalytic Dissecting Adaptive Potential - Phlyogenetics analysis - Published 05 Jun 2014
We describe two versions of COBRA-seq: First, Genome-Wide COBRA (GW-COBRA) that uses PCR to exponentially amplify the sequencing library fragments after linker ligation. Second, Linear Amplification C... moreOBRA (LA-COBRA) that relies on T7 RNA polymerase-mediated transcription yielding many RNA transcripts of the library fragments generated in a linear manner which are subsequently converted to cDNA. The COBRA-seq library protocol is largely adapted to provide robust coverage of the human genome, however, all of the steps are applicable to both model and non-model organisms.
SIEF: Nutritional Genomics - COBRA-seq: Sensitive and Quantitative Methylome Profiling - Published 29 Sep 2015
The DEW pipeline is a one command line solution that aligns reads, corrects expression biases (eXpress), TMM normalizes (edgeR) and produces FPKM values that are then visualized with pretty ggplot gra... morephics.
This BZ2-compressed tar archive provides the software and licensing statements. DEW is written in Perl and requires a SQLite database and is supported for Linux 64-bit computers. The homepage of the software can be found at http://dew.sourceforge.net.less
Cont to TCP01 Dissecting Adaptive - transcriptomics software development - Published 06 Jan 2015
The aim of the project was to generate a high-quality reference transcriptome for Murray-Darling rainbowfish to enable the design of genome-wide expression analysis strategies (such as microarrays) an... mored to obtain protein-coding sequences for nuclear receptors and steroid biosynthetic enzymes involved in sexual development and reproduction. Assembled transcripts, predicted coding regions, deduced proteins and tentative descriptions are available in this collection.less
CLSD-Molecular biomarkers in rainbow - RNA-Seq - Published 06 Nov 2015
De novo assembled transcriptome was developed from leaf samples of wild-type (wt) and high oil (HO) parent (plants metabolically engineered to produce oil in leaf tissues). This was used as a referenc... moree for differential expression analysis of wt vs HO.less
Oil Content - Molecular responses underlying engineered lipid synthesis in leaf tissues - Published 17 Jun 2016
Transcriptome assembly of reads generated individually from the fruit coat, tallow and seed tissues of Chinese tallow fruits harvested at stage 4 (before maturity). The un-assembled reads from individ... moreual tissues were deposited at NCBI-Short Read Archive under accession numbers SRR1653572, SRR1653574 and SRR1653576.less
CLSD EF-RP3 CDF25.1 CESRE TSOP 2013/2014 - experiment - Published 02 Dec 2014
Raw sequencing reads and final assembled contigs associated with the 454 pyrosequencing of the stressor associated transcriptome of the gill and digestive gland of the Sydney Rock Oyster (Saccostrea g... morelomerata). Original .fasta and .qual files are included, as well as the final assembly as described in the paper (Hook et al., Marine Genomics, to be submitted).less
1177.2 Estuarine Health Assessment - Experiment - Published 15 Aug 2014
Raw sequencing reads and final assembled contigs associated with the 454 sequencing of the toxicant responsive transcriptome of the amphipod Melita plumulosa. Original .fasta and .qual files are incl... moreuded, as well as the contigs associated with the final assembly as desribed in the paper (Hook et al., to be submitted, BMC Genomics)less
1177.2 Estuarine Health Assessment - Experiment - Published 24 May 2013
LipiD-QuanT is novel label-free lipid droplet quantification technique to monitor lipid dynamics, based on automated image analysis of phase contrast microscopy images.
SIEF: Nutritional Genomics - LipiD-QuanT Image Analysis Tool - Published 14 Sep 2015
To develop tools to be better able to study toxicological response and immune suppression in Barramundi, Lates calcarfier, we described the transcriptome in the liver and head kidney following immune ... morestimulation. less
Dev immunotoxicological tools to evaluat - Transcriptome discovery - Published 28 Nov 2016
Description of Triadica sebifera trnascripts mapped to Ricinus communis transcript sequences downloaded from Ricinus PlantGDB (http://www.plantgdb.org/RcGDB/)
CLSD EF-RP3 CDF25.1 CESRE TSOP 2013/2014 - Annotation and Taxnomic distribution of Chinese tallow (Triadica sebifera) transcriptome - Published 15 Apr 2015