seqtk

seqtk processes FASTA and FASTQ sequence data (including gzip-compressed files) to perform format parsing, filtering, conversion, and basic sequence manipulations for NGS preprocessing and quality control.

Key Features:

• Format compatibility: Parses FASTA and FASTQ formats and reads gzip-compressed files without prior decompression.
• Data filtering: Filters reads by size and quality and removes reads containing non-designated bases.
• Adapter and mismatch handling: Searches for mismatches against adapter sequences to identify reads for trimming or removal.
• Trimming: Performs trimming at both ends of reads.
• Duplicate removal: Detects and removes duplicate reads.
• Format conversion: Converts FASTQ to FASTA, discarding quality score information when requested.
• Sequence manipulation: Computes reverse complements and converts DNA sequences to RNA.
• Summary statistics: Generates summary statistics for unfiltered and filtered datasets.

Scientific Applications:

• NGS preprocessing: Prepares raw sequencing reads for downstream analysis by performing quality filtering, trimming, and format conversion.
• Variant calling: Produces filtered and trimmed read sets to reduce artifacts that can affect variant calling accuracy.
• Transcriptome assembly: Generates quality-controlled input reads and format conversions needed for transcriptome assembly workflows.
• Metagenomic profiling: Supplies filtered and de-duplicated reads to improve taxonomic and functional profiling in metagenomic analyses.

Methodology:

Parses FASTA/FASTQ (including gzip), filters reads by size and quality, searches mismatches against adapter sequences, trims reads at both ends, removes duplicates and reads with non-designated bases, converts FASTQ to FASTA, computes reverse complements and DNA→RNA conversions, and generates summary statistics for unfiltered and filtered datasets.