cshl_fastx_reverse_complement

cshl_fastx_reverse_complement computes the reverse complement of nucleotide sequences in FASTA and FASTQ files, reversing associated FASTQ quality scores to maintain sequence–quality correspondence.

Key Features:

• Reverse Complementation: Reverses nucleotide order and substitutes bases using complement rules (A ↔ T, C ↔ G) for each sequence.
• FASTA and FASTQ Support: Accepts and processes sequence libraries in both FASTA and FASTQ formats.
• Quality Score Handling in FASTQ: Reverses per-base quality-score strings in FASTQ files to preserve alignment with reverse-complemented sequences.
• Integration with Galaxy Project: Operates within the Galaxy ecosystem for execution and workflow integration.

Scientific Applications:

• Primer design and PCR: Generates reverse-complement sequences needed for design of primers and verification of target strands.
• Sequence analysis and epigenetics: Facilitates analysis of palindromic sequences and studies involving DNA methylation patterns that require strand-specific sequence manipulation.

Methodology:

Reads FASTA or FASTQ input, applies reverse-complement transformation to each sequence (A ↔ T, C ↔ G), reverses FASTQ quality-score lines when present, and writes output preserving file format and attributes while running within Galaxy for workflow tracking.