https://github.com/omicscode/pansam
rust samtools with added features
https://github.com/omicscode/pansam
bioinformatics genome-analysis genome-assembly genome-sequencing rust-lang samtools
Last synced: 5 days ago
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rust samtools with added features
- Host: GitHub
- URL: https://github.com/omicscode/pansam
- Owner: sciencegenome
- License: mit
- Created: 2024-12-09T19:27:37.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2025-01-24T18:19:08.000Z (9 months ago)
- Last Synced: 2025-01-24T19:24:09.020Z (9 months ago)
- Topics: bioinformatics, genome-analysis, genome-assembly, genome-sequencing, rust-lang, samtools
- Language: Rust
- Homepage:
- Size: 5.77 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# pansam
- all rust-samtools combined into a single application specific for the long read technologies and async threaded.
```
cargo build
```
```
Usage: pansam
Commands:
generateid generate ids for all the samtools id present in the samfile
generateidrange generate ids for the specific range in the samtools file
extractor extracts the specific ids from the samfile
viewer view the color coded reads for the specific region
tag-viewer view the colour coded regions for the tags
sam-up-down-align-view upstream and downstream regions,prankaligner and visualization of the alignments
sam-up-down-align allows for the extraction of the upstream and downstream regions from the samfile
filter allows for the filtering of the samfile
filter-range allows for the filtering of the samfile with specified range
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
```
Gaurav Sablok \
Instytut Chemii Bioorganicznej Polskiej Akademii Nauk \
ul. Noskowskiego 12/14 | \
61-704, Poznań Poland