https://github.com/jrhawley/bio-jtools-rs

A suite of bioinformatics tools for interacting with high throughput sequencing (HTS) data, written entirely in Rust
https://github.com/jrhawley/bio-jtools-rs

bioinformatics cli command-line genome-sequencing genomics hts rust-lang

Last synced: 3 months ago
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A suite of bioinformatics tools for interacting with high throughput sequencing (HTS) data, written entirely in Rust

• Host: GitHub
• URL: https://github.com/jrhawley/bio-jtools-rs
• Owner: jrhawley
• License: mit
• Created: 2020-01-12T21:17:16.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2023-11-28T21:42:55.000Z (almost 2 years ago)
• Last Synced: 2025-05-30T14:40:47.634Z (4 months ago)
• Topics: bioinformatics, cli, command-line, genome-sequencing, genomics, hts, rust-lang
• Language: Rust
• Size: 70.9 MB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# bio-jtools-rs

A suite of bioinformatics tools for interacting with high throughput sequencing (HTS) data, written entirely in Rust

![Crates.io](https://img.shields.io/crates/v/bio-jtools)

## Suite

### info

Extract and print metadata about an HTS file.

For FASTQs, this includes number of bases, number of records, and all the instruments the records come from.

### filter

Filter an HTS file by its query names.

Currently only implemented for SAM/BAM files

### jaccard

Calculate the Jaccard index for each pair in a set of BED files.

Can save the results in a comma-separated file, if specified.

### org

Organize a batch of raw sequencing data.

This takes a folder directly from an Illumina sequencer with FASTQ files and organizes them as follows, ready for alginment and quality control:

```shell

YYMMDD_INSTID_RUN_FCID/

├── FASTQs/                     # home for your raw data

    ├── Sample1_R1.fastq.gz

    ├── Sample1_R2.fastq.gz

    └── ...

├── Aligned/                    # a home for your aligned data

├── Reports/                    # QC reports, etc files

├── config.tsv                  # a table of samples (rows) x features (cols)

├── cluster.yaml                # a yaml file of cluster parameters for jobs in the Snakefile

├── README.md                   # description of the folder, data contents

├── setup.log                   # a log of what operations were performed with `bjt org`

└── Snakefile                   # Snakemake workflow file

```