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Parallel / multithreading / multiple threads version of Prinseq
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README.md

Prinseq Parallel

This script handles parallel execution of Prinseq.
It currently supports Prinseq commands for FASTQ files.

Basic functionality

  • Split input FASTQ into multiple files based on a specified number of threads
  • Process each split FASTQ individually
  • Merge processed files

Installation

git clone https://github.com/spabinger/prinseq_parallel.git
cd prinseq_parallel
./INSTALL

This will install prinseq_parallel, prinseq, and coreutils (used for splitting the input file(s))

Usage

./prinseq_parallel.sh FASTQ_FILE (FASTQ_FILE R2) OUT_BASE_PATH TYPE NUM_THREADS TYPE = [SE, PE]

Example: ./prinseq_parallel.sh -no_qual_header -min_qual_mean 20 -trim_left 5 -trim_right 5 -log /output/file.log /input/r1.fastq /input/r2.fastq /output/output/ PE 6

Todo

  • Merge out_bad files
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