fqseqname

fqseqname extracts and lists sequence identifiers from FASTQ formatted files to facilitate tracking and preprocessing of high-throughput sequencing data.

Key Features:

• FASTQ File Compatibility: Processes standard FASTQ formatted files produced by high-throughput sequencing workflows.
• Sequence Identifier Extraction: Extracts and lists sequence names or identifiers from FASTQ records for tracking, indexing, and downstream selection.

Scientific Applications:

• Data Management: Provides sequence identifier lists for organizing and referencing large genomic datasets.
• Workflow Integration: Invokes identifier extraction within Galaxy-based pipelines and can be automated via the Galaxy API or the Bioblend library.
• Metagenomic Analysis: Supplies sequence identifiers required by metagenomic workflows such as MetaGenSense.
• Phylogenetic Studies: Ensures correct identification of sequences prior to phylogenetic analyses in services like NGphylogeny.fr.

Methodology:

Executed within the Galaxy@Pasteur instance where Galaxy serves as the execution engine and manages tool execution on the Institut Pasteur cluster via the Galaxy API or the Bioblend library; integration into Galaxy workflows and web-service pipelines is supported.