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

Result code in 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>

Result on the web

<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>

Result language

angličtina

Original language name

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

Original language description

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.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10606 - Microbiology

Project

<a href="/en/project/LM2015055" target="_blank" >LM2015055: Center for Systems Biology</a><br>

Continuities

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

Publication year

2018

Confidentiality

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

Name of the periodical

Bioinformatics

ISSN

1367-4803

e-ISSN

—

Volume of the periodical

34

Issue of the periodical within the volume

13

Country of publishing house

GB - UNITED KINGDOM

Number of pages

3

Pages from-to

2292-2294

UT code for WoS article

000438247800084

EID of the result in the Scopus database

2-s2.0-85050808964