2 unstable releases
|0.1.5||Oct 21, 2020|
#67 in Biology
43 downloads per month
A suite of bioinformatics tools for interacting with high throughput sequencing (HTS) data, written entirely in Rust
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 an HTS file by its query names. Currently only implemented for SAM/BAM files
Calculate the Jaccard index for each pair in a set of BED files. Can save the results in a comma-separated file, if specified.
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