bbmap.md

BBMap repair.sh Guide

Purpose

• Fixes unpaired FASTQ files by matching read pairs and ensuring proper pairing

Basic Usage

repair.sh in1=input_R1.fastq.gz in2=input_R2.fastq.gz out1=fixed_R1.fastq.gz out2=fixed_R2.fastq.gz

Key Parameters

• in1: Forward reads input file
• in2: Reverse reads input file
• out1: Fixed forward reads output
• out2: Fixed reverse reads output

Example

repair.sh in1=merged_R1.fastq.gz in2=merged_R2.fastq.gz out1=HG001_fixed_R1.fastq.gz out2=HG001_fixed_R2.fastq.gz

Features

• Automatically identifies and matches read pairs
• Handles gzipped or uncompressed files
• Preserves read order
• Removes orphaned reads