STINGRAY: system for integrated genomic resources and analysis

Abstract

BackgroundThe STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms.FindingsSTINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation.ConclusionSTINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/.

Picoplankton Bloom in Global South? A High Fraction of Aerobic Anoxygenic Phototrophic Bacteria in Metagenomes from a Coastal Bay (Arraial do Cabo—Brazil)

“…The SFF files generated were analyzed on Stingray ( ) (Wagner et al, 2014 ) to generate the clipped FASTA and QUAL files. The CD-HIT-454 (Niu et al, 2010 ) program was used to remove artificial duplicates (artifacts) using default parameters, and LUCY v1.20 (Chou et al, 2001 ) (default parameters) was applied to remove low quality and small sequences (<20 Phred score, <100 base pairs [bp]).…”

The Comparative Genomics and Phylogenomics of Leishmania Amazonensis Parasite

“…The multifasta files of the assembled L. amazonensis genome were submitted to STINGRAY pipeline (Wagner, et al, 2014) 28 ( http://stingray.biowebdb.org ), an improved version of the original GARSA 29 system, for semi-automatic annotation. The STINGRAY pipeline and a TblastX 30 approach were used by transferring the L. mexicana 21 annotation to L. amazonensis , which was further improved by the identification of conserved domains.…”

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“…The sequenced data were analyzed on the Stingray@Galaxy platform. 22 The quality of the sequenced samples was evaluated by FastQC 0.67. 23 For data cleaning, Trimmommatic was used with cutoff above 38 and minimum length 20.…”

“…The data were processed and analyzed in Stingray@ Galaxy. 22 FAST STASTIC version 1.0.0 was used for statistical verification. The median value of each file was considered for filtering the sequences by Filter sequences by length.…”