一、软件介绍：

hifiadapterfilt：将 .bam 转换为 .fastq 并删除带有剩余 PacBio 接头序列的读数。

开发语言：Shell

源码地址：https://github.com/sheinasim/HiFiAdapterFilt/archive/refs/tags/v2.0.0.tar.gz

二、安装步骤：

1、依赖安装：

yum install cmake gcc-c++

2、bamtools安装：

cd /path/to/bamtools

wget https://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.2.tar.gz

tar xf v2.5.2.tar.gz

cd bamtools-2.5.2

mkdir build && cd build

cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/bamtools

make -j

make install

export PATH=/path/to/bamtools/bin:$PATH

export LD_LIBRARY_PATH=/path/to/bamtools/lib64:$LD_LIBRARY_PATH

export INCLUDE=/path/to/bamtools/include:$INCLUDE

3、blast+安装：

cd /path/to/blast

wget http://mirror.ufs.ac.za/blast/executables/blast%2B/2.9.0/ncbi-blast%2B-2.9.0-src.tar.gz

tar xf ncbi-blast+-2.9.0-src.tar.gz

cd ncbi-blast-2.9.0+-src

export BLAST_TOP=`pwd`

cd $BLAST_TOP

wget https://github.com/LMDB/lmdb/archive/refs/tags/LMDB_0.9.24.tar.gz

tar xf LMDB_0.9.24.tar.gz

export LMDB_PATH=$BLAST_TOP/lmdb-LMDB_0.9.24

cd $BLAST_TOP/c++

CC=gcc CXX=g++ ./configure

cd ReleaseMT/build

make all_r -j

export PATH=$BLAST_TOP/c++/ReleaseMT/bin:$PATH

4、hifiadapterfilt安装：

cd /path/to/hifiadapterfilt

wget https://github.com/sheinasim/HiFiAdapterFilt/archive/refs/tags/v2.0.0.tar.gz

tar xf v2.0.0.tar.gz

cd HiFiAdapterFilt-2.0.0

sed -i "6s/HiFiAdapterFilt/HiFiAdapterFilt-2.0.0/g" pbadapterfilt.sh

export PATH=`pwd`:$PATH

export PATH=`pwd`/DB:$PATH

三、软件验证：

cd /path/to/hifiadapterfilt/HiFiAdapterFilt-2.0.0

cp /path/to/bamtools/bamtools-2.5.2/tests/data/sam_spec_example.bam .

pbadapterfilt.sh -t 8

在当前目录下生成4个文件“sam_spec_example.blocklist”、“sam_spec_example.contaminant.blastout”、“sam_spec_example.filt.fastq.gz”、“sam_spec_example.stats”。