k-SLAM:k-mer Sorted List Alignment and Metagenomics
2017-02-27 21:25
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k-SLAM 是基于大量高通量宏基因组序列数据分析的比对程序,它基于k-mer技术上在reads和序列之间进行比较,然后用Smith-Waterman算法验证。校准是连接在一起组成一个伪组装用来提高特异性。用LCA技术推断如何分类。从sam格式校准和输出文件中可以找出基因和突变。k-SLAM是快速高度并行的,每分钟可处理500万的150bp的双端reads数据。
News:k-slam中install_slam_new_db.sh 可以下载最新的NCBI参考基因组。注意:这些数据中包含了很多基因组,这将会增加执行时间和内存的需求。
类型:Desktop app
k-SLAM 说明:
https://github.com/aindj/k-SLAM
测试:
编译:
数据库构建:
测试:
News:k-slam中install_slam_new_db.sh 可以下载最新的NCBI参考基因组。注意:这些数据中包含了很多基因组,这将会增加执行时间和内存的需求。
类型:Desktop app
k-SLAM 说明:
https://github.com/aindj/k-SLAM
测试:
编译:
cd k-SLAM/ cd build/ make mv build/SLAM ./ export PATH=$PATH:.
数据库构建:
install_slam.sh database_dir bacteria viruses
测试:
./SLAM --db ./database_dir/ --output-file /project/meta_benchmark/Result/Reuslt_test/2k-slam.out /project/meta_benchmark/Data/mergepe_out.fq cd /project/meta_benchmark/Result/Reuslt_test/
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