https://github.com/applicativesystem/rust-samtools-genomecapture

rust samtools genomecapture
https://github.com/applicativesystem/rust-samtools-genomecapture

bioinformatics genome-analysis genome-analysis-annotation genome-assembly genome-bioinformatics genome-mapper genome-sequencing

Last synced: 7 days ago
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rust samtools genomecapture

• Host: GitHub
• URL: https://github.com/applicativesystem/rust-samtools-genomecapture
• Owner: applicativesystem
• License: mit
• Created: 2024-12-03T19:17:05.000Z (19 days ago)
• Default Branch: main
• Last Pushed: 2024-12-03T19:19:20.000Z (19 days ago)
• Last Synced: 2024-12-03T20:27:09.532Z (19 days ago)
• Topics: bioinformatics, genome-analysis, genome-analysis-annotation, genome-assembly, genome-bioinformatics, genome-mapper, genome-sequencing
• Language: Rust
• Homepage:
• Size: 6.84 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# rust-samtools-genomecapture

- rust samtools genomecapture.

- give the id list, reference genome, upstream and downstream and extracts the reference genome portion for the genome browser. 

-  rust-samtools-genome-capture: takes a genome alignment files, a reference fasta file, the upstream and the downstream regions 

- targetd capture assay development for taking reads from HybSeq.

- general note: Incase of Golang and RUST, please see the last commit message and if it says compiled binary then it is completed or else still in development version.

```

cargo build 

```

```

λ gauravsablok rust-samtools-genomecapture → λ git main* → ./target/debug/rust-samtools-genome-capture -h

Usage: rust-samtools-genome-capture      

Arguments:

     please provide the path to the alignment file

        please provide the id list for the specific region

         please provide the fasta file used for the reference alignment

      please provide the upstream add from the sam alignments to be extracted

    please provide the downstream add from the sam alignments to be extracted

    please provide the readlength of the sequencing reads

Options:

  -h, --help     Print help

  -V, --version  Print version

```

- how to run the binary

```

./rust-samtools-genome-capture ./sample-files/Col0_C1.100k_selected.sam ./sample-files/idlist.txt ./sample-files/sample-fasta.fasta 5 10

``

- result from the rust-samtools-genome-capture

```

- selected-ids-downstream.fasta - downstream for those ids 

- selected-ids-reads.fasta - reads aligned to those ids.

- selected-ids-upstream.fasta - upstreams for those ids.

- selected-ids-upstream-region-downstream.fasta - upstream-region -downstream for those ids.

```

Gaurav Sablok