fastq_rs
Fastq cli toolkit, aiming to an alternative to seqkit.
Requirements
- Linux OS (Ubuntu 24.04.2)
- Rust >= 1.90.0
Install from source
Clone the repository or download the source code. Enter the fastq_rs directory and run:
cargo build --release
The generated binary is available in target/release/fastq_rs.
Usage
Run with:
fastq_rs <subcommand> <args>
fastq_rs stats
Calculate basic stats.
fastq_rs stats --fastq <reads.fastq.gz> <optional_args>
Note - if no file is provided, fastq_rs will read from stdin (plain FASTQ).
Optional arguments:
fastq_rs sanitize
Attempt to sanitize malformatted reads.
fastq_rs sanitize --fastq <reads.fastq.gz> <optional_args>
Optional arguments:
fastq_rs head
Output the first n reads.
fastq_rs head --fastq <reads.fastq.gz> <optional_args>
Optional arguments:
fastq_rs grep
Search and filter read ids by regular expressions.
fastq_rs grep --fastq <reads.fastq.gz> --pattern <regex_string> <optional_args>
Optional arguments:
fastq_rs concat
Sanitize and concat fastq files. This feature is probably slower than using normal bash commands like zcat *.fastq.gz | pigs -f > concat.fastq.gz, but has the advantage of skipping malformatted records.
fastq_rs concat --fastqs <reads.fastq.gz> <...> <optional_args>
Optional arguments:
fastq_rs sort
Sort reads based on provided metric.
fastq_rs sort --fastq <reads.fastq.gz> <optional_args>
Optional arguments:
fastq_rs fq2-fa
Convert FASTQ to FASTA.
fastq_rs fq2-fa --fastq <reads.fastq.gz> <optional_args>
Optional arguments:
fastq_rs fq2-tab
Convert FASTQ to a .tsv file with information about each read. If compiled with the plot feature, will generate a read scatter and boxplot.
fastq_rs fq2-tab --fastq <reads.fastq.gz> <optional_args>
Optional arguments:
fastq_rs filter
Filter reads.
fastq_rs filter --fastq <reads.fastq.gz> <optional_args>
Optional arguments:
fastq_rs sample
Sample reads by fraction or number of reads.
fastq_rs sample --fastq <reads.fastq.gz> <optional_args>
Optional arguments:
fastq_rs trim
Trim reads through fuzzy search with ambiguous nucleotide support.
fastq_rs trim --fastq <reads.fastq.gz> <optional_args>
Optional arguments: