HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees
Summary: Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics. We developed HybPhyloMaker, a bioinformatics pipeline that performs target enrichment data analysis from raw reads to supermatrix-, supertree-, and multispecie...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2018-01-01
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| Series: | Evolutionary Bioinformatics |
| Online Access: | https://doi.org/10.1177/1176934317742613 |
| _version_ | 1819111284020346880 |
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| author | Tomáš Fér Roswitha E Schmickl |
| author_facet | Tomáš Fér Roswitha E Schmickl |
| author_sort | Tomáš Fér |
| collection | DOAJ |
| description | Summary: Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics. We developed HybPhyloMaker, a bioinformatics pipeline that performs target enrichment data analysis from raw reads to supermatrix-, supertree-, and multispecies coalescent-based species tree reconstruction. HybPhyloMaker is written in BASH and integrates common bioinformatics tools. It can be launched both locally and on a high-performance computer cluster. Compared with existing target enrichment data analysis pipelines, HybPhyloMaker offers the following main advantages: implementation of all steps of data analysis from raw reads to species tree reconstruction, calculation and summary of alignment and gene tree properties that assist the user in the selection of “quality-filtered” genes, implementation of several species tree reconstruction methods, and analysis of the coding regions of organellar genomes. Availability: The HybPhyloMaker scripts, manual as well as a test data set, are available in https://github.com/tomas-fer/HybPhyloMaker/ . HybPhyloMaker is licensed under open-source license GPL v.3 allowing further modifications. |
| first_indexed | 2024-12-22T03:55:10Z |
| format | Article |
| id | doaj.art-19efaf21ef6241d4a59a67642ab6e227 |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-22T03:55:10Z |
| publishDate | 2018-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-19efaf21ef6241d4a59a67642ab6e2272022-12-21T18:39:53ZengSAGE PublishingEvolutionary Bioinformatics1176-93432018-01-011410.1177/1176934317742613HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species TreesTomáš Fér0Roswitha E Schmickl1Department of Botany, Faculty of Science, Charles University, Prague, Czech RepublicInstitute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic.Summary: Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics. We developed HybPhyloMaker, a bioinformatics pipeline that performs target enrichment data analysis from raw reads to supermatrix-, supertree-, and multispecies coalescent-based species tree reconstruction. HybPhyloMaker is written in BASH and integrates common bioinformatics tools. It can be launched both locally and on a high-performance computer cluster. Compared with existing target enrichment data analysis pipelines, HybPhyloMaker offers the following main advantages: implementation of all steps of data analysis from raw reads to species tree reconstruction, calculation and summary of alignment and gene tree properties that assist the user in the selection of “quality-filtered” genes, implementation of several species tree reconstruction methods, and analysis of the coding regions of organellar genomes. Availability: The HybPhyloMaker scripts, manual as well as a test data set, are available in https://github.com/tomas-fer/HybPhyloMaker/ . HybPhyloMaker is licensed under open-source license GPL v.3 allowing further modifications.https://doi.org/10.1177/1176934317742613 |
| spellingShingle | Tomáš Fér Roswitha E Schmickl HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees Evolutionary Bioinformatics |
| title | HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees |
| title_full | HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees |
| title_fullStr | HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees |
| title_full_unstemmed | HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees |
| title_short | HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees |
| title_sort | hybphylomaker target enrichment data analysis from raw reads to species trees |
| url | https://doi.org/10.1177/1176934317742613 |
| work_keys_str_mv | AT tomasfer hybphylomakertargetenrichmentdataanalysisfromrawreadstospeciestrees AT roswithaeschmickl hybphylomakertargetenrichmentdataanalysisfromrawreadstospeciestrees |