tgv

Crates.iotgv
lib.rstgv
version
sourcesrc
created_at2025-03-31 00:22:00.685415+00
updated_at2025-04-13 02:09:08.117503+00
descriptionExplore genomes in the terminal. Light, blazing fast 🚀, vim-motion.
homepage
repository
max_upload_size
id1612897
Cargo.toml error:TOML parse error at line 23, column 1 | 23 | autolib = false | ^^^^^^^ unknown field `autolib`, expected one of `name`, `version`, `edition`, `authors`, `description`, `readme`, `license`, `repository`, `homepage`, `documentation`, `build`, `resolver`, `links`, `default-run`, `default_dash_run`, `rust-version`, `rust_dash_version`, `rust_version`, `license-file`, `license_dash_file`, `license_file`, `licenseFile`, `license_capital_file`, `forced-target`, `forced_dash_target`, `autobins`, `autotests`, `autoexamples`, `autobenches`, `publish`, `metadata`, `keywords`, `categories`, `exclude`, `include`
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Zeqian Li (zeqianli)

documentation

README

Terminal Genome Viewer

Explore omics data without leaving the terminal.

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

https://github.com/user-attachments/assets/b250f901-8e4d-4d5d-b150-fa9195b08e14

TGV is at a very early stage. Please don't rely on it for your papers (yet) :)

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

Installation

See Installation

Quick start

# 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

View alignments

# 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

Supported formats (see wiki):

  • BAM (index and sorted; .bai file is needed): local, AWS S3, HTTP, FTP, Google Cloud

Contribution is welcome!

See wiki. Also join the Discord to discuss ideas.

FAQ

  • 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?

Commit count: 0

cargo fmt