源代码编译安装velvets
apt-get默认安装的velvet最大km值只有31；源代码编译安装的话可以修改这个值到127
# 源码编译安装velvet
# cd ~/Biosofts/
# wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
tar zvxf /disk/shares/velvet_1.2.10.tgz -C ~/Biosofts/
cd ~/Biosofts/velvet_1.2.10/
make 'CATEGORIES=10' 'MAXKMERLENGTH=127' 'LONGSEQUENCES=1' 'OPENMP=1' 'BUNDLEDZLIB=1'
./velveth -h
最后一步./velveth -h返回截图如上
比较不同kmer值对velvet组装结果的影响
nano kmerselection.sh
#输入如下代码
################################
#!/bin/bash
Data1=/disk/shares/Seqs/test_7942raw_1.fq.gz
Data2=/disk/shares/Seqs/test_7942raw_2.fq.gz
Velvet_dir=~/Biosofts/velvet_1.2.10
for k in `seq 23 8 127`;do
mkdir velvet$k
$Velvet_dir/velveth velvet$k $k -shortPaired -fastq -separate $Data1 $Data2
$Velvet_dir/velvetg velvet$k -exp_cov auto -cov_cutoff auto -very_clean yes
done
############################
./kmerselection.sh
最后一步运行结果
Quast安装
#预编译安装
tar zvxf /disk/shares/quast-5.0.0.tar.gz -C ~/Biosofts/
#进入软件目录
cd Biosofts/quast-5.0.0/
#测试是否可以运行
./quast.py
#添加环境变量
echo 'export PATH=~/Biosofts/quast-5.0.0:$PATH' >> ~/.bashrc
source ~/.bashrc
比较不同km值拼接效果
quast.py -o
compare_velvet_kmer
velvet23/contigs.fa
velvet31/contigs.fa
velvet39/contigs.fa
velvet47/contigs.fa
velvet55/contigs.fa
velvet63/contigs.fa
velvet71/contigs.fa
velvet79/contigs.fa
velvet87/contigs.fa
velvet95/contigs.fa
velvet103/contigs.fa
velvet111/contigs.fa
velvet119/contigs.fa
velvet127/contigs.fa
Quast截图
Quast结果
Quast结果
