BBMerge安装及使用

本文主要使用BBMerge合并双端序列为单端序列文件，便于后续处理。

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BBTools官网

BBMerge手册

BBMerge是BBTools中的一个工具。

bbduk – filters or trims reads for adapters and contaminants using k-mers
bbmap – short-read aligner for DNA and RNA-seq data
bbmerge – merges overlapping or nonoverlapping pairs into a single reads
reformat – converts sequence files between different formats such as fastq and fasta

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一、安装

wget https://udomain.dl.sourceforge.net/project/bbmap/BBMap_38.98.tar.gz
tar xvzf BBMap_38.98.tar.gz

二、使用

首先查看bbmerge使用细则

cd bbmap
less bbmerge.sh

Input may be stdin or a file, fasta or fastq, raw or gzipped

#Usage for paired files
bbmerge.sh in1=<read1> in2=<read2> out=<merged reads> outu1=<unmerged1> outu2=<unmerged2>
#Usage for interleaved files
bbmerge.sh in=<reads> out=<merged reads> outu=<unmerged reads>

三、实战练习

/home/liuxin/bbmap/bbmerge.sh in1=D2124163A_122_1.fq.gz in2=D2124163A_122_2.fq.gz out=merged outu1=unmerged1 outu2=unmerged2

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