FN Archimer Export Format
PT J
TI getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories
BT 
AF Moco, Vincent
   Cazenave, Damien
   Garnier, Maëlle
   Pot, Matthieu
   Marcelino, Isabel
   Talarmin, Antoine
   Guyomard-Rabenirina, Stéphanie
   Breurec, Sébastien
   Ferdinand, Séverine
   Dereeper, Alexis
   REYNAUD, Yann
   Couvin, David
AS 1:1;2:1;3:1;4:1;5:1;6:1;7:1;8:1,2,3;9:1;10:1;11:1;12:1;
FF 1:;2:;3:;4:;5:;6:;7:;8:;9:;10:;11:;12:;
C1 Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
   Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles, Pointe-à-Pitre, France
   Centre d’Investigation Clinique Antilles Guyane, Inserm CIC 1424, Pointe-à-Pitre, France
C2 INST PASTEUR, FRANCE
   UNIV ANTILLES, FRANCE
   INSERM, FRANCE
IN DOAJ
IF 3
TC 1
UR https://archimer.ifremer.fr/doc/00788/89999/96740.pdf
   https://archimer.ifremer.fr/doc/00788/89999/96742.xls
   https://archimer.ifremer.fr/doc/00788/89999/96743.xls
LA English
DT Article
DE ;Genome sequences;Nucleotide diversity;Assembly;DNA;Repository;Metadata
AB Background Biological sequences are increasing rapidly and exponentially worldwide. Nucleotide sequence databases play an important role in providing meaningful genomic information on a variety of biological organisms. Results The getSequenceInfo software tool allows to access sequence information from various public repositories (GenBank, RefSeq, and the European Nucleotide Archive), and is compatible with different operating systems (Linux, MacOS, and Microsoft Windows) in a programmatic way (command line) or as a graphical user interface. getSequenceInfo or gSeqI v1.0 should help users to get some information on queried sequences that could be useful for specific studies (e.g. the country of origin/isolation or the release date of queried sequences). Queries can be made to retrieve sequence data based on a given kingdom and species, or from a given date. This program allows the separation between chromosomes and plasmids (or other genetic elements/components) by arranging each component in a given folder. Some basic statistics are also performed by the program (such as the calculation of GC content for queried assemblies). An empirically designed nucleotide ratio is calculated using nucleotide information in order to tentatively provide a “NucleScore” for studied genome assemblies. Besides the main gSeqI tool, other additional tools have been developed to perform various tasks related to sequence analysis. Conclusion The aim of this study is to democratize the use of public repositories in programmatic ways, and to facilitate sequence data analysis in a pedagogical perspective. Output results are available in FASTA, FASTQ, Excel/TSV or HTML formats. The program is freely available at: https://github.com/karubiotools/getSequenceInfo. getSequenceInfo and supplementary tools are partly available through the recently released Galaxy KaruBioNet platform (http://calamar.univ-ag.fr/c3i/galaxy_karubionet.html). 
PY 2022
PD JUN
SO Bmc Bioinformatics
SN 1471-2105
PU Springer Science and Business Media LLC
VL 23
IS 1
UT 000822352100003
DI 10.1186/s12859-022-04809-5
ID 89999
ER

EF