bio-jtools-rs

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

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. Not currently implemented.

jaccard

Calculate the Jaccard index for each pair in a set of BED files. Not currently implemented.

kspec

Calculate the k-mer spectra of an HTS file. Not currently implemented.

org

Organize a batch of raw sequencing data.

This takes a folder directly from an Illumina sequencer with FASTQ files and organizes them into the following directories: * FASTQs * Aligned * Reports

Benchmarking

Benchmarks on run in a Windows 10 computer, Intel i5 750 @ 2.67 GHz processor with 12 GB of RAM. Times are listed +/- standard deviation, using hyperfine --warmup 2.

info

| File | # Reads | t_gzip | t_plain | | ---------------------- | ------- | -------------------- | --------------------- | | examples/SRR0000001.fastq | 2 500 | 17.0 ms +/- 0.9 ms | 12.8 ms +/- 1.0 ms | | examples/SRR0000002.fastq | 25 000 | 78.4 ms +/- 3.3 ms | 16.6 ms +/- 0.6 ms | | M_abscessus_HiSeq.fq | 5 682 010 | 12.323 s +/- 0.227 s | 951.5 ms + 5.6 ms |