metaSPAdes,megahit,IDBA-UB:宏基因组装软件安装与使用

metaSPAdes,megahit,IDBA-UB是目前比较主流的宏基因组组装软件

metaSPAdes安装

GitHub - ablab/spades: SPAdes Genome Assembler

#3.15.5的预编译版貌似有问题，使用源码安装试试
wget http://cab.spbu.ru/files/release3.15.5/SPAdes-3.15.5.tar.gz
tar -xzf SPAdes-3.15.5.tar.gz
cd SPAdes-3.15.5
./spades_compile.sh

~/bin/metaspades.py -1 pe_1.fq -2 pe_2.fq -t 180 --memory 450 -o out_dir

megahit安装 

 https://github.com/voutcn/megahit

wget https://github.com/voutcn/megahit/releases/download/v1.2.9/MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz
tar zvxf MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz
cd MEGAHIT-1.2.9-Linux-x86_64-static/bin/
./megahit --test

./megahit --min-contig-len 500 -t 180 -1 pe_1.fq -2 pe_2.fq -o out.fasta

IDBA-UD安装

GitHub - loneknightpy/idba

wget https://github.com/loneknightpy/idba/releases/download/1.1.3/idba-1.1.3.tar.gz
tar -xzvf idba-1.1.3.tar.gz
cd idba-1.1.3
./configure
make
~/bin/idba

 IDBA-UD默认最长只支持reads长度为128的序列，需要修改

如果你的reads序列大于128，可修改 ~/idba-1.1.3/src/sequence/short_sequence.h文件中的kMaxShortSequence值（我改成了150）

cd idba-1.1.3
./configure
make

#IDBA-UD只能输入fasta，所以先把序列合并
~/bin/fq2fa --merge --filter read_1.fq read_2.fq read.fa 
#运行
~/bin/idba_ud --pre_Correction --min_contig 500 --num_threads 180 --mink 90 --maxk 124 -r read.fa -o output_dir