#bioinformatics #cli #fastq

app bio-jtools

A suite of bioinformatics tools for interacting with high throughput sequencing (HTS) data

2 unstable releases

2022.6.6 Jun 7, 2022
2021.1.21 Jan 21, 2021
2020.10.21 Oct 21, 2020
2020.6.11 Jun 11, 2020
0.1.5 Oct 21, 2020

#67 in Biology

43 downloads per month

MIT license

82KB
1.5K SLoC

bio-jtools-rs

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

Crates.io

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:

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

Dependencies

~10–14MB
~258K SLoC