SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F18%3A00492157" target="_blank" >RIV/61388971:_____/18:00492157 - isvavai.cz</a>

Výsledek na webu

<a href="http://dx.doi.org/10.1093/bioinformatics/bty071" target="_blank" >http://dx.doi.org/10.1093/bioinformatics/bty071</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/bioinformatics/bty071" target="_blank" >10.1093/bioinformatics/bty071</a>

Jazyk výsledku

angličtina

Název v původním jazyce

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses

Popis výsledku v původním jazyce

Motivation: Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use. We created SEED 2, a graphical user interface for handling high-throughput amplicon-sequencing data under Windows operating systems. nResults: SEED 2 is the only sequence visualizer that empowers users with tools to handle amplicon-sequencing data of microbial community markers. It is suitable for any marker genes sequences obtained through Illumina, IonTorrent or Sanger sequencing. SEED 2 allows the user to process raw sequencing data, identify specific taxa, produce of OTU-tables, create sequence alignments and construct phylogenetic trees. Standard dual core laptops with 8 GB of RAM can handle ca. 8 million of Illumina PE 300 bp sequences, ca. 4 GB of data. nAvailability and implementation: SEED 2 was implemented in Object Pascal and uses internal functions and external software for amplicon data processing. SEED 2 is a freeware software, available at http://d360prx.biomed.cas.cz:2305/mbu/lbwrf/seed/as a self-contained file, including all the dependencies, and does not require installation. Supplementary data contain a comprehensive list of supported functions.

Název v anglickém jazyce

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses

Popis výsledku anglicky

Motivation: Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use. We created SEED 2, a graphical user interface for handling high-throughput amplicon-sequencing data under Windows operating systems. nResults: SEED 2 is the only sequence visualizer that empowers users with tools to handle amplicon-sequencing data of microbial community markers. It is suitable for any marker genes sequences obtained through Illumina, IonTorrent or Sanger sequencing. SEED 2 allows the user to process raw sequencing data, identify specific taxa, produce of OTU-tables, create sequence alignments and construct phylogenetic trees. Standard dual core laptops with 8 GB of RAM can handle ca. 8 million of Illumina PE 300 bp sequences, ca. 4 GB of data. nAvailability and implementation: SEED 2 was implemented in Object Pascal and uses internal functions and external software for amplicon data processing. SEED 2 is a freeware software, available at http://d360prx.biomed.cas.cz:2305/mbu/lbwrf/seed/as a self-contained file, including all the dependencies, and does not require installation. Supplementary data contain a comprehensive list of supported functions.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10606 - Microbiology

Projekt

<a href="/cs/project/LM2015055" target="_blank" >LM2015055: Centrum pro systémovou biologii</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2018

Kód důvěrnosti údajů

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

Název periodika

Bioinformatics

ISSN

1367-4803

e-ISSN

—

Svazek periodika

34

Číslo periodika v rámci svazku

13

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

3

Strana od-do

2292-2294

Kód UT WoS článku

000438247800084

EID výsledku v databázi Scopus

2-s2.0-85050808964