CLI

Six commands for common workflows, accessible via seqchain <command>:

Command	Purpose
seqchain design	CRISPR guide design from a genome file
seqchain count	Barcode counting from FASTQ reads
seqchain score	Mismatch variant scoring for guides
seqchain tnseq	Tn-seq insertion profiling from FASTQ
seqchain serve	Start the REST API server
seqchain demo atacflux	Generate ATF1 CRISPRa demo data

Examples

# Design guides for a genome
seqchain design yeast.gb --preset spcas9 --output guides.tsv

# Count barcodes
seqchain count library.fa reads_R1.fq.gz reads_R2.fq.gz --output counts.tsv

# Start API server
seqchain serve --host 0.0.0.0 --port 8000

# Generate demo data
seqchain demo atacflux --output-dir ./atacflux_data

main

SeqChain CLI — composable genomic sequence analysis.

Seven subcommands:

• seqchain design — CRISPR guide design
• seqchain count — barcode counting
• seqchain score — mismatch variant scoring
• seqchain tnseq — Tn-seq insertion profiling
• seqchain process — NGS processing (align, peaks, signal, counts)
• seqchain serve — start the REST API server
• seqchain demo atacflux — ATF1 CRISPRa demo data generator