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