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Shrink Reads

Summary

Subset FASTQ reads by count or fraction for lightweight test datasets.

Description

Supports deterministic head-style subsampling (first_n) and random sampling (random) for single-end, interleaved, and paired-end layouts.

This command is intended for quick dry runs and resource-reduced tests, not as a full read-normalization strategy.

Usage

rolypoly shrink-reads [OPTIONS]

Options

  • -i, -in, --input: Input raw reads file(s) or directory containing them. For paired-end reads, you can provide an interleaved file or the R1 and R2 files separated by comma. (type: TEXT; default: Sentinel.UNSET)
  • -st, --subset-type: how to sample reads from input. (type: CHOICE; default: top_reads)
  • -sz, --sample-size: Will only return (at most) this much reads (if <1, will be interpreted as a proportion of total reads, else as the exact number of reads to get) (type: FLOAT; default: 1000)
  • -g, --log-file: Path to save loggging message to. defaults to current folder. (type: PATH; default: /clusterfs/jgi/scratch/science/metagen/neri/code/rolypoly/rolypoly.log)
  • -ll, --log-level: Log level. Options: debug, info, warning, error, critical (type: CHOICE; default: info)