seqfu

seqfu provides utilities for manipulating FASTA and FASTQ files and performing sequence-level quality control and preprocessing for next-generation sequencing (NGS) data.

Key Features:

• FASTA and FASTQ support: Provides a comprehensive suite of commands for manipulation of FASTA and FASTQ file formats.
• Interleave/deinterleave FASTQ: Implements high-performance interleave and deinterleave operations for FASTQ files.
• Illumina lane merging: Merges Illumina lanes to consolidate sequencing runs into single datasets.
• Quality control — degenerate primer identification: Detects degenerate primers within sequence datasets as part of QC procedures.
• Quality control — length statistics and extraction: Computes length statistics and extracts specific portions of datasets for analysis.
• Dereplication with provenance tracking: Dereplicates sequences across multiple files while tracking provenance of each sequence.
• High-performance implementations: Provides optimized implementations for common sequence file operations to handle large NGS datasets.

Scientific Applications:

• NGS preprocessing: Preprocesses FASTQ datasets for downstream analyses in genomics and metagenomics workflows.
• Lane consolidation: Consolidates Illumina lanes to produce unified datasets for variant calling or assembly.
• Quality assessment: Identifies problematic primers and assesses length distributions to inform data filtering and trimming.
• Dereplication and traceability: Performs sequence dereplication across files while preserving provenance for reproducibility and validation.

Methodology:

Implemented in Nim and providing high-performance implementations for interleave/deinterleave operations, Illumina lane merging, dereplication across multiple files with provenance tracking, and quality-control functions including degenerate primer identification, length statistics, and sequence extraction on FASTA/FASTQ files.