Quick Start

Get up and running with checkle in 5 minutes.

Basic Commands

Hash a single file

checkle hash genome.fastq.gz

Hash multiple files

checkle hash *.fastq.gz

Hash with SHA-256 instead of MD5

checkle hash --algo sha256 genome.fastq.gz

Save checksums to a file

checkle hash *.fastq.gz -o checksums.txt

Verification

Verify a single file

checkle verify genome.fastq.gz --hash d41d8cd98f00b204e9800998ecf8427e

Verify multiple files from a checksum file

checkle verify-many --checksum-file checksums.txt

Working with Directories

Hash all files in a directory recursively

checkle hash /data/sequencing_run --recursive

Hash only specific file types

checkle hash /data --recursive --include "*.fastq" --include "*.fasta"

Exclude certain patterns

checkle hash /data --recursive --exclude "*.tmp" --exclude "*.log"

Archive Support

Hash files inside a TAR archive without extracting

checkle hash data.tar.gz:sequences/sample.fastq

Hash all files in an archive

checkle hash data.tar.gz:*

Output Formats

JSON output for downstream processing

checkle hash *.bam --format json > checksums.json

CSV for spreadsheet import

checkle hash *.vcf --format csv > checksums.csv

Pretty table display

checkle hash *.fastq --pretty

Performance Tuning

Increase parallel readers for large files

checkle hash huge_genome.fasta --parallel-readers 16

Adjust chunk size for optimal performance

checkle hash *.bam --chunk-size-kb 4096

Next Steps