Data

Data for hybpiper2-nf and resolve_paralogs-nf: Containerization and additional options for assembly and paralog detection in target enrichment data

Commonwealth Scientific and Industrial Research Organisation
Schmidt-Lebuhn, Alexander ; McLay, Todd ; Jackson, Chris
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.25919/nb45-8w35&rft.title=Data for hybpiper2-nf and resolve_paralogs-nf: Containerization and additional options for assembly and paralog detection in target enrichment data&rft.identifier=https://doi.org/10.25919/nb45-8w35&rft.publisher=Commonwealth Scientific and Industrial Research Organisation&rft.description=This is an example dataset of 24 species of Pycnosorus and Australian Craspedia to illustrate the functionality of hybpiper2-nf and resolve_paralogs-nf, two Nextflow scripts and associated Singularity container developed for the Genomics for Australian Plants consortium's phylogenomic pillar Australian Angiosperms Tree of Life.Lineage: DNA extraction from herbarium specimens or silica-dried leaf samples. Library prep. Target capture using the Angiosperms353 bait kit. Illumina sequencing. Trimmomatic, HybPiper assembly, paralog resolution using gene tree topology, concatenation, likelihood analysis in iqtree2.&rft.creator=Schmidt-Lebuhn, Alexander &rft.creator=McLay, Todd &rft.creator=Jackson, Chris &rft.date=2022&rft.edition=v1&rft_rights=Creative Commons Attribution 4.0 International Licence https://creativecommons.org/licenses/by/4.0/&rft_rights=Data is accessible online and may be reused in accordance with licence conditions&rft_rights=All Rights (including copyright) CSIRO 2022.&rft_subject=bioinformatics&rft_subject=Craspedia&rft_subject=target capture&rft_subject=sequence enrichment&rft_subject=Pycnosorus&rft_subject=Asteraceae&rft_subject=Compositae&rft_subject=Gnaphalieae&rft_subject=paralogy&rft_subject=paralogs&rft_subject=orthology&rft_subject=orthologs&rft_subject=assembly&rft_subject=Plant and fungus systematics and taxonomy&rft_subject=Evolutionary biology&rft_subject=BIOLOGICAL SCIENCES&rft.type=dataset&rft.language=English Access the data
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Creative Commons Attribution 4.0 International Licence
https://creativecommons.org/licenses/by/4.0/

Data is accessible online and may be reused in accordance with licence conditions

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This is an example dataset of 24 species of Pycnosorus and Australian Craspedia to illustrate the functionality of hybpiper2-nf and resolve_paralogs-nf, two Nextflow scripts and associated Singularity container developed for the Genomics for Australian Plants consortium's phylogenomic pillar Australian Angiosperms Tree of Life.
Lineage: DNA extraction from herbarium specimens or silica-dried leaf samples. Library prep. Target capture using the Angiosperms353 bait kit. Illumina sequencing. Trimmomatic, HybPiper assembly, paralog resolution using gene tree topology, concatenation, likelihood analysis in iqtree2.

Available: 2022-09-21

Data time period: 2020-07-01 to 2022-09-21

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Subjects
Asteraceae | Biological Sciences | Compositae | Craspedia | Evolutionary Biology | Gnaphalieae | Plant and Fungus Systematics and Taxonomy | Pycnosorus | assembly | bioinformatics | orthologs | orthology | paralogs | paralogy | sequence enrichment | target capture |

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Identifiers
ACN 633 798 857