宏基因组分析4-宏基因组组装(MEGAHIT,IDBA)

MegaHit
http://www.l3-bioinfo.com/products/megahit.html
https://github.com/voutcn/megahit

安装

sudo apt install g++ zlib1g-dev git make cmake


cd /home/llt/software
git clone https://github.com/voutcn/megahit.git
cd megahit
git submodule update --init
mkdir build && cd build
cmake .. -DCMAKE_BUILD_TYPE=Release 
make -j4
make simple_test
sudo make install

运行

sudo apt install python
/home/llt/software/megahit/megahit --12 /home/llt/test/data/clean/SRR1976948_1p,/home/llt/test/data/clean/SRR1976948_2p --min-contig-len 300 -o assembly

idba

/software/idba/bin/fq2fa --merge --filter ssg1_30m.1.fq ssg1_30m.2.fq ssg1_30m.fa
/software/idba/bin/idba_ud -o assembly_idba-ud -r ssg1_30m.fa --maxk 124 --num_threads 8 --min_contig 300