Documentation
Complete reference guides and tutorials for Kaidoku tools and pipelines. Learn how to use each tool and pipeline, understand parameters, and interpret results.
Getting Started
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Pipelines
Genome Assembly Pipeline
Complete genomic workflow: quality control, trimming, and de novo assembly of sequencing reads to produce assembled contigs
assemblyView docs →
Variant Calling Pipeline
Comprehensive variant detection workflow: quality control, read alignment to reference genome, and identification of SNPs, insertions, and deletions with detailed annotation
variantsView docs →
Metagenomics Pipeline
Identify pathogens in samples: quality control, taxonomic profiling, and pathogen flagging using MetaPhlAn or Kraken2. Flags bacteria, viruses, and fungi of clinical concern.
metagenomicsView docs →
RNA-Seq Pipeline
Complete RNA-Seq workflow: quality control, alignment with STAR, and gene quantification with featureCounts for transcriptome analysis
transcriptomicsView docs →
analysis
Codon Usage
Analyze codon usage frequency and bias in DNA/RNA sequences
FreeView docs →
GC Content
Calculate GC content and nucleotide composition
FreeView docs →
FastQC
Quality control for high-throughput sequencing data (FASTQ): per-base quality, sequence content, GC content, and more.
FreeView docs →
Consensus Sequence
Generate consensus sequence from multiple sequences
FreeView docs →
Motif Finder
Find consensus motifs in DNA/RNA sequences
PremiumView docs →
Metagenomics
Analyze microbial communities from sequencing data
PremiumView docs →
Variant Calling
Identify genetic variants in sequencing data
PremiumView docs →
ORF Finder
Find all Open Reading Frames (ORFs) in DNA sequences
FreeView docs →
Restriction Enzyme Analysis
Identify restriction enzyme cut sites and calculate fragment sizes
FreeView docs →
Primer Design
Design optimal PCR primers with comprehensive quality analysis
PremiumView docs →
Genome Browser
Interactive genome browser with sequence visualization and annotation tracks
PremiumView docs →