https://github.com/applicativesystem/rust-fastp-clipped
rust implementation of the tilled window approach
https://github.com/applicativesystem/rust-fastp-clipped
bioinformatics bioinformatics-analysis bioinformatics-data genome-analysis genome-annotation illumina-sequencing
Last synced: 7 months ago
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rust implementation of the tilled window approach
- Host: GitHub
- URL: https://github.com/applicativesystem/rust-fastp-clipped
- Owner: applicativesystem
- License: mit
- Created: 2024-11-30T07:44:57.000Z (7 months ago)
- Default Branch: main
- Last Pushed: 2024-12-09T18:54:19.000Z (7 months ago)
- Last Synced: 2024-12-09T19:39:36.328Z (7 months ago)
- Topics: bioinformatics, bioinformatics-analysis, bioinformatics-data, genome-analysis, genome-annotation, illumina-sequencing
- Language: Rust
- Homepage:
- Size: 4.88 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# rust-window-clipped
- rust implementation of the tilled window approach for dropping the adapters.
- instead of looking at each base, scans the read using the length of the adapter so that it becomes fast iterative.
- first drops the bases and then uses a iteration to clip the reads with in memory and no read and write multiple times.
```
cargo build
```
- how to run the binary
```
λ gauravsablok rust-fastp-clipped → λ git main* → ./target/debug/rust-window-clipped -h
Usage: rust-window-clipped
Arguments:
please provide the reads R1 file path
please provide the reads R2 file path
please provide the quality value to be used as a threshold
please provide the adapter sequence
Options:
-h, --help Print help
-V, --version Print version
```
Gaurav Sablok