amplab实验室的SNAP算法运行和操作

amplab实验室的SNAP算法运行和操作：

环境：ubuntu14.04

1.安装：

参考【1】和【2】，需要：

g++ version 4.6
zlib 1.2.8 from http://zlib.net/

安装：

sudo apt-get install g++
sudo apt-get install zlib1g-dev


zlib没有直接的安装包，

2.编译：在snap目录下运行make

3.操作：

（1）构建参考基因的索引：

./snap-aligner index tests/datatest/datatest.fa index1运行结果：
hadoop@Mcnode1:~/cloud/adam/xubo/snap$ ./snap-aligner index tests/datatest/datatest.fa index1
Welcome to SNAP version 1.0beta.22.

Hash table slack 0.300000
Loading FASTA file 'tests/datatest/datatest.fa' into memory...0s
Saving genome...0s
Computing bias table.
Bias computation: 0 / 1202
Computed bias table in 0s
Allocating memory for hash tables...0s
Building hash tables.
0(0%) seeds occur more than once, total of 0(0%) genome locations are not unique, 498(41%) bad seeds, 0 both complements used 500 no string
Hash table build took 0s
Building overflow table.
Overflow table build and hash table save took 0s
Saving overflow table...0s
Index build and save took 0s (1202 bases/s)


（2）比对：

单端比对：

./snap-aligner single index1 tests/datatest/datatest.fq -o output.sam


运行结果：
hadoop@Mcnode1:~/cloud/adam/xubo/snap$ ./snap-aligner single index1 tests/datatest/datatest.fq -o output.sam
Welcome to SNAP version 1.0beta.22.

Loading index from directory... 0s. 1202 bases, seed size 20
Aligning.
Total Reads Aligned, MAPQ >= 10 Aligned, MAPQ < 10 Unaligned Too Short/Too Many Ns %Pairs Reads/s Time in Aligner (s)
2 2 (100.00%) 0 (0.00%)

双端比对：
./snap-aligner paired index1 tests/datatest/datatest.fq tests/datatest/datatest.fq -o output2.sam

运行结果：

hadoop@Mcnode1:~/cloud/adam/xubo/snap$ ./snap-aligner paired index1 tests/datatest/datatest.fq tests/datatest/datatest.fq -o output2.sam
Welcome to SNAP version 1.0beta.22.

Loading index from directory... 0s. 1202 bases, seed size 20
Aligning.
Total Reads Aligned, MAPQ >= 10 Aligned, MAPQ < 10 Unaligned Too Short/Too Many Ns %Pairs Reads/s Time in Aligner (s)
4 4 (100.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0.00%% 1,000 0


4.其他：snap文件夹下的docs有教程

参考文献：

【1】 https://github.com/amplab/snap
【2】 http://snap.cs.berkeley.edu/