xgt

git clone https://github.com/Ebedthan/xgt.git
cd xgt
cargo build --release
# binary is at target/release/xgt
cp target/release/xgt ~/.local/bin/

# Search all genomes assigned to a genus
xgt search g__Escherichia

# Search at species level (names with spaces are handled automatically)
xgt search 's__Escherichia coli' -F org --type --id

# Get the full card for a genome
xgt genome GCA_000005845.2

# Get the taxonomic classification of a taxon
xgt taxon g__Escherichia

# Compare a genome's taxonomy between two GTDB releases
xgt diff GCA_000005845.2 --from R214 --to R220

# Run a batch diff and cache results, repeat runs are instant
xgt diff -f accessions.txt --from R214 --to R232 -O csv -o changes.csv

# Check cache statistics
xgt --cache-info

# Check if a newer version of xgt is available
xgt --check-update

# Force a fresh fetch even though the cache has a valid entry
xgt genome GCA_000005845.2 --no-cache

# See how much space the cache is using
xgt --cache-info

# Clear all cached data
xgt --clear-cache

# Search for a genus, output as JSON
xgt search g__Escherichia -O json

# Search at species level, spaces in names are handled automatically
xgt search 's__Escherichia coli' -F org

# Search from a file, output TSV to a file
xgt search -f genera.txt -O tsv -o results.tsv

# Restrict to species representatives, print accessions only
xgt search g__Bacillus --rep --id

# Pipe accessions directly to xgt genome
xgt search g__Rhizobium --id | xgt genome -f - -O csv -o rhizobium.csv

# Full genome card
xgt genome GCA_000005845.2

# Taxonomic history across all GTDB releases
xgt genome GCA_000005845.2 --history

# Batch: process accessions from a file, write CSV
xgt genome -f accessions.txt -O csv -o results.csv

# Batch: write one JSON file per accession
xgt genome -f accessions.txt --split --split-dir genome_cards/

# Target a specific GTDB release
xgt genome GCA_000005845.2 --release R214

# Force a fresh fetch, bypassing the cache
xgt genome GCA_000005845.2 --no-cache

# Full taxonomic record for a genus
xgt taxon g__Escherichia

# Species-level query with spaces in the name
xgt taxon 's__Escherichia coli'

# Search for a taxon name in the current release
xgt taxon --search Escherichia

# Search across all GTDB releases and NCBI
xgt taxon --search --all Escherichia

# List all genomes in a taxon
xgt taxon g__Escherichia --genomes

# List only species representatives
xgt taxon g__Escherichia --genomes --reps

# Compare a genome between two releases
xgt diff GCA_000005845.2 --from R214 --to R220

# Compare against the latest release
xgt diff GCA_000005845.2 --from R214

# Batch comparison, CSV output, cached on subsequent runs
xgt diff -f accessions.txt --from R214 --to R232 -O csv -o changes.csv

# Find which genomes changed between two GTDB releases
# Results are cached, the second run returns instantly
xgt diff -f study_accessions.txt --from R214 --to R220 \
  -O csv -o taxonomy_changes.csv

# Filter to only changed genomes
awk -F',' '$4 == "true"' taxonomy_changes.csv

# Get all representative accessions for a genus, then fetch genome cards
xgt search g__Rhizobium --rep --id | xgt genome -f - -O csv -o rhizobium.csv

# One JSON file per genome
xgt genome -f accessions.txt --split --split-dir results/

# One diff file per accession
xgt diff -f accessions.txt --from R214 --split --split-dir diffs/

# Check what is cached and how much space it uses
xgt --cache-info

# Clear the cache entirely (e.g. after a new GTDB release)
xgt --clear-cache

# Force fresh data for a single query without clearing the whole cache
xgt genome GCA_000005845.2 --no-cache

# Bash
xgt completions bash > ~/.local/share/bash-completion/completions/xgt

# Zsh (ensure ~/.zfunc is in your fpath)
xgt completions zsh > ~/.zfunc/_xgt

# Fish
xgt completions fish > ~/.config/fish/completions/xgt.fish