https://github.com/codecreatede/rust-genome-longread-count

datastructure rustlang faster iteration for genome, short and long reads
https://github.com/codecreatede/rust-genome-longread-count

bioinformatics genome-classification genome-informatics rust-crate rust-lang sequence-classification sequencing-data

Last synced: about 2 months ago
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datastructure rustlang faster iteration for genome, short and long reads

• Host: GitHub
• URL: https://github.com/codecreatede/rust-genome-longread-count
• Owner: codecreatede
• Created: 2024-10-21T19:23:40.000Z (2 months ago)
• Default Branch: main
• Last Pushed: 2024-11-04T12:01:26.000Z (about 2 months ago)
• Last Synced: 2024-11-04T13:17:39.820Z (about 2 months ago)
• Topics: bioinformatics, genome-classification, genome-informatics, rust-crate, rust-lang, sequence-classification, sequencing-data
• Language: Rust
• Homepage:
• Size: 4.27 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# rust-genome-longread-count

- A kmer origin finding faster than the recent implementation of the recent implementation. Back to sequences: Find the origin of 𝑘-mers DOI: 10.21105/joss.07066.

- output a table for the direct ingestion into any graphs. 

- outputs a sam type file with the distinct count of the kmers and can be used for the jellyfish count. 

- support both the genome and the longread fasta file. 

```

Usage: kmerorigin  

Arguments:

         please provide the kmer to be searched for the origin

    please provide the path to be searched for the strings containing the kmer

Options:

  -h, --help     Print help

  -V, --version  Print version

```

- a better table for direct ingestion into the graphs also to make a jellyfish count. 

```

./target/debug/kmerorigin 4 ./sample-files/fastafile.fasta

>seq1

AGTCAGTC        AGTC    0       4

AGTCAGTC        GTCA    1       5

AGTCAGTC        CAGT    3       7

AGTCAGTC        TCAG    2       6

>seq2

AGGCAGTC        CAGT    3       7

AGGCAGTC        GGCA    1       5

AGGCAGTC        AGGC    0       4

AGGCAGTC        GCAG    2       6

```

Gaurav Sablok