Butcher

Butcher is designed to trim reads for single-end long-read sequencing (like Nanopore) and paired-end Illumina sequencing. Similar to other tools such as Nanofilt, Porechop, and Trimmomatic, Butcher excels in trimming low-quality regions from the ends of reads, detecting and removing adapter sequences, and eradicating poly-A and poly-G tracks from sequencing reads. A standout feature of Butcher is its ability to provide a preview of the changes directly in the terminal. This lets users see the expected results before they decide to proceed with the operation.

Getting butcher

Downloads are available on the release page for Linux systems, or you can build it (see below).

Documentation

You want to preserve color annotations in piped processes, and you'll need to set the command line coloring option. For bash this looks something like export CLICOLOR_FORCE=1. This will then color the output when previewing your cut reads.

A constrained use-case fastq trimmer

Usage: butcher [OPTIONS]

Options:
      --fastq1 <FASTQ1>
          the first fastq file -- required
      --fastq2 <FASTQ2>
          a second fastq file, for Illumina paired-end reads
      --out-fastq1 <OUT_FASTQ1>
          output fastq file 1
      --out-fastq2 <OUT_FASTQ2>
          output fastq file 2 -- if using paired-end reads
      --minimum-remaining-read-size <MINIMUM_REMAINING_READ_SIZE>
          minimum remaining read size after trimming is complete -- reads shorter than this will be discarded [default: 10]
      --window-min-qual-score <WINDOW_MIN_QUAL_SCORE>
          the minimum average quality score a window of nucleotides must have [default: 10]
      --window-size <WINDOW_SIZE>
          trimming window size [default: 10]
      --trim-poly-a
          enable poly-A tail trimming (seen in RNA-seq data)
      --trim-poly-g
          trim a read after a poly-G tail is found (seen when sequencing off the end of an Illumina read with 2-color chemistry)
      --trim-poly-x-length <TRIM_POLY_X_LENGTH>
          the length of the poly-X tail to trim (use with the poly-A or poly-G trimming) [default: 10]
      --trim-poly-x-proportion <TRIM_POLY_X_PROPORTION>
          the proportion of bases that must be X to trim the read end [default: 0.9]
      --primers <PRIMERS>
          primers to detect and remove (we'll make their reverse complement too), separated by commas
      --primers-max-mismatch-distance <PRIMERS_MAX_MISMATCH_DISTANCE>
          the maximum mismatches allowed for primer trimming -- it's best if this is 1 or 2 [default: 1]
      --primers-end-proportion <PRIMERS_END_PROPORTION>
          what proportion of the read ends can a primer be found in (front or back) -- if it's interior to this margin we drop the read(s) [default: 0.2]
      --preview
          just display the reads and what we'd cut, don't actually write any output to disk
  -h, --help
          Print help

Compiling

Rust nightly is required to avoid the crash text when you pipe (|) butcher on the command line. Building with nightly is simple:

cargo build --release

From the command line. A butcher artifact will be created in the target/release/ folder.