https://github.com/sciencegenome/samtools-viewer
rust samtools viewer
https://github.com/sciencegenome/samtools-viewer
bioinformatics genome-alingment genome-analysis genome-bioinformatics genome-sequencing rustlang samtools
Last synced: 4 months ago
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rust samtools viewer
- Host: GitHub
- URL: https://github.com/sciencegenome/samtools-viewer
- Owner: sciencegenome
- License: mit
- Created: 2024-12-06T21:05:47.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2025-01-15T20:51:22.000Z (9 months ago)
- Last Synced: 2025-01-17T09:12:25.118Z (9 months ago)
- Topics: bioinformatics, genome-alingment, genome-analysis, genome-bioinformatics, genome-sequencing, rustlang, samtools
- Language: Rust
- Homepage:
- Size: 3.57 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# rust-samtools-viewer
- rust samtools view.
- given an sam alignment file and a give range of the coordinate from the genome, will produce a colour coded alignment for the reads aligned in that region.
- Especially important for showing the reads specific to abundance, metabolites, genomic association to phenotypes.
- please see the last commit message and if it says compiled binary then it is completed or else still in development version.
- This feature is not present in samtools.
- explanation : The first read related to the normal phenotype, the second to the diseased one and the third one to the mutant and so on.
```
cargo build
```
```
Usage: rust-samtools-viewer
Arguments:
please provide the path to the alignment file
please provide the genome capture region start
please provide the genome capture region end
Options:
-h, --help Print help
-V, --version Print version
```
- sample view from the sample alignment, choose any number or coordinate from your aligned file.
```
./target/debug/rust-samtools-viewer ./sample-files/alignreads.sam 200 250
```
Gaurav Sablok