transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F23%3A00571021" target="_blank" >RIV/61388963:_____/23:00571021 - isvavai.cz</a>

Výsledek na webu

<a href="https://doi.org/10.1186/s12859-023-05254-8" target="_blank" >https://doi.org/10.1186/s12859-023-05254-8</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s12859-023-05254-8" target="_blank" >10.1186/s12859-023-05254-8</a>

Jazyk výsledku

angličtina

Název v původním jazyce

transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation

Popis výsledku v původním jazyce

BACKGROUND: RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different software tools. The complexity of these de novo transcriptomics workflows therefore presents a major barrier for researchers to adopt best-practice methods and up-to-date versions of software. RESULTS: Here we present a streamlined and universal de novo transcriptome assembly and annotation pipeline, transXpress, implemented in Snakemake. transXpress supports two popular assembly programs, Trinity and rnaSPAdes, and allows parallel execution on heterogeneous cluster computing hardware. CONCLUSIONS: transXpress simplifies the use of best-practice methods and up-to-date software for de novo transcriptome assembly, and produces standardized output files that can be mined using SequenceServer to facilitate rapid discovery of new genes and proteins in non-model organisms.

Název v anglickém jazyce

transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation

Popis výsledku anglicky

BACKGROUND: RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different software tools. The complexity of these de novo transcriptomics workflows therefore presents a major barrier for researchers to adopt best-practice methods and up-to-date versions of software. RESULTS: Here we present a streamlined and universal de novo transcriptome assembly and annotation pipeline, transXpress, implemented in Snakemake. transXpress supports two popular assembly programs, Trinity and rnaSPAdes, and allows parallel execution on heterogeneous cluster computing hardware. CONCLUSIONS: transXpress simplifies the use of best-practice methods and up-to-date software for de novo transcriptome assembly, and produces standardized output files that can be mined using SequenceServer to facilitate rapid discovery of new genes and proteins in non-model organisms.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

<a href="/cs/project/GM21-11563M" target="_blank" >GM21-11563M: Mapování chemodiverzity pepřovníkovitých rostlin pomocí nové generace platformy MZmine</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2023

Kód důvěrnosti údajů

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

Název periodika

BMC Bioinformatics

ISSN

1471-2105

e-ISSN

1471-2105

Svazek periodika

24

Číslo periodika v rámci svazku

1

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

11

Strana od-do

133

Kód UT WoS článku

000964450400006

EID výsledku v databázi Scopus

2-s2.0-85151795606