converttranscriptfile_fastqtofasta

converttranscriptfile_fastqtofasta converts FastQ sequencing files to FASTA by extracting sequence identifiers and nucleotide sequences for downstream analyses.

Key Features:

• Format Conversion: Converts FastQ files, which include nucleotide sequences and quality scores, into FASTA files containing only nucleotide sequences and identifiers.
• Galaxy Integration: Executes within the Galaxy execution engine and can run on the Institut Pasteur compute cluster.
• API Communication: Interacts with Galaxy via the Galaxy API or the Bioblend library to manage jobs and data transfer.

Scientific Applications:

• Metagenomic Analysis: Prepares sequence datasets in FASTA format for metagenomic workflows that require sequence-only input.
• Phylogenetic Studies: Generates FASTA-formatted sequences for phylogenetic inference and evolutionary analyses.
• General Bioinformatics Research: Produces FASTA files for gene annotation, homology searches, and comparative genomics.

Methodology:

Extracts sequence identifiers and nucleotide sequences from FastQ files and formats them into FASTA; runs within the Galaxy execution engine on the Institut Pasteur cluster and communicates via the Galaxy API or Bioblend.