Explore omics data without leaving the terminal.

Light, blazing fast 🚀, vim motion, memory safe.

https://github.com/user-attachments/assets/ce33b31d-d3eb-4395-9ab4-ab3a501aa1be

(TGV is at an early statge. Please don't rely your papers on it (yet) :)

Contribution and bug reports are welcome! Please join the Discord to discuss ideas.)

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

# Add Rust to your path (or restart your terminal):
source "$HOME/.cargo/env"

cargo install tgv

# Clone the repository
git clone https://github.com/zeqianli/tgv.git
cd tgv

cargo install --path .

# Browse the hg38 human genome. Internet connection required.
tgv

• Quit: :q
• Movement:
  • Left / down / up / right: h/j/k/l:
  • Faster left / right: y/p
  • Next gene / previous gene / next exon / previous exon: W/B/w/b
  • Repeat movements: _number_ + _movement_ (e.g. 20B: left by 20 genes)
• Zoom in / out: z/o
• Go to gene: :_gene_ (e.g. :TP53)
• Go to a chromosome position: :_chr_:_position_: (e.g. :1:2345)

Full key bindings and comparison with Vim.

# View BAM file aligned to the hg19 human reference genome
tgv sorted.bam -g hg19

# Start at a coordinate
tgv sorted.bam -r 12:25398142 -g hg19

# View a indexed remote BAM, starting at TP53, using the hg38 reference genome
tgv s3://my-bucket/sorted.bam -r TP53

# Use --no-reference for non-human alignments
# (Sequence / feature display not supported yet)
tgv non_human.bam -r 1:123 --no-reference

• BAM (index and sorted). .bai file is needed.
  • Local, AWS, Google Cloud, or HTTP/HTTPS
  • Local: place the .bai file in the same directory; or specify the index file with -i.
  • s3: set credentials in environmental variables. See: https://www.htslib.org/doc/htslib-s3-plugin.html
  • gss: TODO not tested. Please provide feedback if it works!
  • Note that the custom bai path (-i) is not supported for remote use for due to rust-htslib API limitation.

See ROADMAP.md for future plans.

Contribution is welcome. See CONTRIBUTE.md. Please join the Discord to discuss ideas!

• How to quit TGV?
  Just like vim :) Press Esc to ensure you're in normal mode, then type :q and press Enter.

• Where are the reference genome data from?

  • Sequences: UCSC Genome Browser API
  • Annotation: UCSC MariaDB, hg19 / hg38, table ncbiRefSeqSelect (same as IGV)