hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution
Abstract Premise The HybPiper pipeline has become one of the most widely used tools for the assembly of target capture data for phylogenomic analysis. After the production of locus sequences and before phylogenetic analysis, the identification of paralogs is a critical step for ensuring the accurate...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2023-07-01
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| Series: | Applications in Plant Sciences |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/aps3.11532 |
| _version_ | 1828716834054995968 |
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| author | Chris Jackson Todd McLay Alexander N. Schmidt‐Lebuhn |
| author_facet | Chris Jackson Todd McLay Alexander N. Schmidt‐Lebuhn |
| author_sort | Chris Jackson |
| collection | DOAJ |
| description | Abstract Premise The HybPiper pipeline has become one of the most widely used tools for the assembly of target capture data for phylogenomic analysis. After the production of locus sequences and before phylogenetic analysis, the identification of paralogs is a critical step for ensuring the accurate inference of evolutionary relationships. Algorithmic approaches using gene tree topologies for the inference of ortholog groups are computationally efficient and broadly applicable to non‐model organisms, especially in the absence of a known species tree. Methods and Results We containerized and expanded the functionality of both HybPiper and a pipeline for the inference of ortholog groups, providing novel options for the treatment of target capture sequence data, and allowing seamless use of the outputs of the former as inputs for the latter. The Singularity container presented here includes all dependencies, and the corresponding pipelines (hybpiper‐nf and paragone‐nf, respectively) are implemented via two Nextflow scripts for easier deployment and to vastly reduce the number of commands required for their use. Conclusions The hybpiper‐nf and paragone‐nf pipelines are easily installed and provide a user‐friendly experience and robust results to the phylogenetic community. They are used by the Australian Angiosperm Tree of Life project. The pipelines are available at https://github.com/chrisjackson-pellicle/hybpiper-nf and https://github.com/chrisjackson-pellicle/paragone-nf. |
| first_indexed | 2024-03-12T14:19:14Z |
| format | Article |
| id | doaj.art-2133dfefccf54dc896d27d2aec2e87e9 |
| institution | Directory Open Access Journal |
| issn | 2168-0450 |
| language | English |
| last_indexed | 2024-03-12T14:19:14Z |
| publishDate | 2023-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | Applications in Plant Sciences |
| spelling | doaj.art-2133dfefccf54dc896d27d2aec2e87e92023-08-19T21:30:40ZengWileyApplications in Plant Sciences2168-04502023-07-01114n/an/a10.1002/aps3.11532hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolutionChris Jackson0Todd McLay1Alexander N. Schmidt‐Lebuhn2Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne Victoria 3004 AustraliaRoyal Botanic Gardens Victoria, Birdwood Avenue, Melbourne Victoria 3004 AustraliaCentre for Australian National Biodiversity Research CSIRO, Clunies Ross Street Canberra 2601 Australian Capital Territory AustraliaAbstract Premise The HybPiper pipeline has become one of the most widely used tools for the assembly of target capture data for phylogenomic analysis. After the production of locus sequences and before phylogenetic analysis, the identification of paralogs is a critical step for ensuring the accurate inference of evolutionary relationships. Algorithmic approaches using gene tree topologies for the inference of ortholog groups are computationally efficient and broadly applicable to non‐model organisms, especially in the absence of a known species tree. Methods and Results We containerized and expanded the functionality of both HybPiper and a pipeline for the inference of ortholog groups, providing novel options for the treatment of target capture sequence data, and allowing seamless use of the outputs of the former as inputs for the latter. The Singularity container presented here includes all dependencies, and the corresponding pipelines (hybpiper‐nf and paragone‐nf, respectively) are implemented via two Nextflow scripts for easier deployment and to vastly reduce the number of commands required for their use. Conclusions The hybpiper‐nf and paragone‐nf pipelines are easily installed and provide a user‐friendly experience and robust results to the phylogenetic community. They are used by the Australian Angiosperm Tree of Life project. The pipelines are available at https://github.com/chrisjackson-pellicle/hybpiper-nf and https://github.com/chrisjackson-pellicle/paragone-nf.https://doi.org/10.1002/aps3.11532HybPiperNextfloworthologsparalogsphylogenomicsSingularity container |
| spellingShingle | Chris Jackson Todd McLay Alexander N. Schmidt‐Lebuhn hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution Applications in Plant Sciences HybPiper Nextflow orthologs paralogs phylogenomics Singularity container |
| title | hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution |
| title_full | hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution |
| title_fullStr | hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution |
| title_full_unstemmed | hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution |
| title_short | hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution |
| title_sort | hybpiper nf and paragone nf containerization and additional options for target capture assembly and paralog resolution |
| topic | HybPiper Nextflow orthologs paralogs phylogenomics Singularity container |
| url | https://doi.org/10.1002/aps3.11532 |
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