HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F67985939%3A_____%2F18%3A00508675" target="_blank" >RIV/67985939:_____/18:00508675 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216208:11310/18:10386014

Výsledek na webu

<a href="http://hdl.handle.net/11104/0299514" target="_blank" >http://hdl.handle.net/11104/0299514</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1177/1176934317742613" target="_blank" >10.1177/1176934317742613</a>

Jazyk výsledku

angličtina

Název v původním jazyce

HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10611 - Plant sciences, botany

Projekt

—

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2018

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Evolutionary Bioinformatics

ISSN

1176-9343

e-ISSN

—

Svazek periodika

14

Číslo periodika v rámci svazku

January 1

Stát vydavatele periodika

NZ - Nový Zéland

Počet stran výsledku

9

Strana od-do

1-9

Kód UT WoS článku

000424039200001

EID výsledku v databázi Scopus

2-s2.0-85060288952