Terminal Genome Viewer

Explore omics data without leaving the terminal.

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

demo.mp4

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

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

Installation

See Installation

Quick start

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

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

Full key bindings

TGV supports all genomes on the UCSC genome browser:

tgv -g mm10
tgv -g cat
tgv -g covid

# List common genomes
tgv --list

# Or, all UCSC assemblies
tgv --list-more

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

# No reference genome
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?

  • Sequences: UCSC Genome Browser API
  • Annotation: UCSC MariaDB