基因数据处理59之snap运行single-end（1千万条100bp的reads）

记录：

    hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ snap-aligner single snap/snapindex g38L100c10000000Nhs20.fq -o snap/g38L100c10000000Nhs20.snap.sam
    Welcome to SNAP version 1.0beta.23.

    Loading index from directory... 0s.  248957422 bases, seed size 20
    Aligning.
    Total Reads    Aligned, MAPQ >= 10    Aligned, MAPQ < 10     Unaligned              Too Short/Too Many Ns     Reads/s   Time in Aligner (s)
    9,257,464      8,838,906 (95.48%)     411,004 (4.44%)        7,554 (0.08%)          0 (0.00%)                 40,252    230
    hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ snap-aligner single snap/snapindex g38L100c10000000Nhs20.fq -o snap/g38L100c10000000Nhs20.snap2.sam
    Welcome to SNAP version 1.0beta.23.

    Loading index from directory... 12s.  248957422 bases, seed size 20
    Aligning.
    Total Reads    Aligned, MAPQ >= 10    Aligned, MAPQ < 10     Unaligned              Too Short/Too Many Ns     Reads/s   Time in Aligner (s)
    9,257,464      8,838,906 (95.48%)     411,004 (4.44%)        7,554 (0.08%)          0 (0.00%)                 40,171    230
    hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$ 

参考

【1】https://github.com/xubo245/AdamLearning
【2】https://github.com/bigdatagenomics/adam/ 
【3】https://github.com/xubo245/SparkLearning
【4】http://spark.apache.org
【5】http://stackoverflow.com/questions/28166667/how-to-pass-d-parameter-or-environment-variable-to-spark-job  
【6】http://stackoverflow.com/questions/28840438/how-to-override-sparks-log4j-properties-per-driver

研究成果：

【1】 [BIBM] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Chao Wang, and Xuehai Zhou, "Distributed Gene Clinical Decision Support System Based on Cloud Computing", in IEEE International Conference on Bioinformatics and Biomedicine. (BIBM 2017, CCF B)
【2】 [IEEE CLOUD] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Xuehai Zhou. Efficient Distributed Smith-Waterman Algorithm Based on Apache Spark (CLOUD 2017, CCF-C).
【3】 [CCGrid] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Jinhong Zhou, Xuehai Zhou. DSA: Scalable Distributed Sequence Alignment System Using SIMD Instructions. (CCGrid 2017, CCF-C).
【4】more: https://github.com/xubo245/Publications

Help

If you have any questions or suggestions, please write it in the issue of this project or send an e-mail to me: [email protected]
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