Installation

• cargo: cargo install tgv --locked
• brew: brew install zeqianli/tgv/tgv
• bioconda: conda install bioconda::tgv
• Pre-built binaries: Github releases

# Browse the hg38 human genome (internet needed)
tgv

# Or your favorite genome (see `tgv list` or `tgv list --more`)
tgv -g cat 

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

Full key bindings

If you use a reference genome frequently, downloading a local cache is highly recommended. This makes TGV much faster.

# Cache are in ~/.tgv by default.
tgv download hg38

Browse alignments:

# View BAM file aligned to the hg38 human reference genome
tgv sorted.bam

# VCF and BED support
tgv sorted.bam -v variants.vcf -b intervals.bed

# View a indexed remote BAM, starting at TP53, using the hg19 reference genome
tgv s3://my-bucket/sorted.bam -r TP53 -g hg19

# BAM file with no reference genome
tgv non_human.bam -r 1:123 --no-reference

Supported formats

Why?

Browsing alignment files is essential for genomics. Genomics research is often in the terminal (SSH session to HPCs or the cloud). IGV is popular but cumbersome for remote sessions. Terminal-based applications (1, 2) are not as feature-rich. Rust bioinformatics community is vibrant (3 4) and Ratatui makes powerful terminal UIs. So TGV is born!

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

I'm new to Rust and I want a learning project

Contributing to tgv is a great way to learn Rust. There are many small, isolated components that need improvement, some requiring <10 lines of code change. You can find them by searching for FIXME comments. You can also find issues that are extra friendly to new contributors tagged with "contributor friendly".

I have a bug / Something isn't working

Search the issue tracker and discussions for similar issues.If your issue hasn't been reported already, open an issue and make sure to fill in the template completely.

I have an idea for a feature / I've implemented a feature

Thank you. Because TGV is still at an early stage, API changes frequently, so please coordinate with me in the discord / github discussion before starting to avoid large diffs.

• ratatui
• UCSC Genome Browser
• rust-htslib, htslib, noodles, twobit, bigtools