amplab実験室のSNAPアルゴリズムの実行と操作

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雲の計算 amplab SNAP 遺伝子整合 に匹敵
amplab実験室のSNAPアルゴリズムの実行と操作:
環境:ubuntu 14.04
1.インストール:
参考【1】と【2】、必要:
  • g++ version 4.6
  • zlib 1.2.8 from http://zlib.net/

    • インストール:
    sudo apt-get install g++
sudo apt-get install zlib1g-dev

    zlibは直接インストールパッケージがなく、
    2.コンパイル:snapディレクトリの下でmakeを実行する
    3.操作:
    (1)参照遺伝子のインデックスを構築する:
      ./snap-aligner index tests/datatest/datatest.fa index1
    実行結果:
    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)比較:
    シングルエンドペア:
    
 ./snap-aligner single index1 tests/datatest/datatest.fq -o output.sam

    実行結果:
    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%)

    両端ペア:
    ./snap-aligner paired index1 tests/datatest/datatest.fq tests/datatest/datatest.fq -o output2.sam

    実行結果:
    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.その他:snapフォルダの下のdocsにチュートリアルがあります
    参考文献:
    【1】 https://github.com/amplab/snap
    【2】 http://snap.cs.berkeley.edu/
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