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    • A

      图片素材搜集
      • anneng

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      A

      accfbcb2-ee0c-4d81-a2f3-c767256839c3-image.png

    • Z

      天合数据中心第三台服务器信息记录
      • zhanglu

      1
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      7
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    • A

      生信文件格式
      • anneng

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      A

      https://cyrille.rossant.net/moving-away-hdf5/
      Moving away from HDF5 - Cyrille Rossant

      HDF5的缺点也很明显

    • A

      Snakemake
      • anneng

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      A

      https://snakemake.readthedocs.io/en/stable/executing/cloud.html
      snakemake支持tes

    • A

      生信流程框架
      • anneng

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      A

      https://training.seqera.io/ nextflow培训 不错的教材

    • A

      github代理
      • anneng

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      11
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    • I

      win10 Network Location Awareness 错误:1068依赖服务或组无法启动
      • ice-melt

      1
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    • Z

      服务器数据迁移记录
      • zhanglu

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    • Z

      Seqtk、Seqkit两个处理fasta/fastq的神器
      • zhanglu

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    • A

      blast
      • anneng

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      A

      https://open.oregonstate.education/computationalbiology/chapter/command-line-blast/
      blast的一个教程

    • I

      服务器GPU配置
      • ice-melt

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      A

      nvidia-smi
      Failed to initialize NVML: Driver/library version mismatch
      cat /var/log/dpkg.log | grep nvidia
      2021-07-26 06:50:34 status installed nvidia-driver-460:amd64 460.91.03-0ubuntu0.18.04.1

      系统自动进行了一次升级 重启即可!

      用这个帖子的办法可以不重启
      https://stackoverflow.com/questions/43022843/nvidia-nvml-driver-library-version-mismatch#comment73133147_43022843

      How can we do that?
      First, we should know which drivers are loaded.

      lsmod | grep nvidia
      You may get

      nvidia_uvm 634880 8
      nvidia_drm 53248 0
      nvidia_modeset 790528 1 nvidia_drm
      nvidia 12312576 86 nvidia_modeset,nvidia_uvm
      Our final goal is to unload nvidia mod, so we should unload the module depend on nvidia:

      sudo rmmod nvidia_drm
      sudo rmmod nvidia_modeset
      sudo rmmod nvidia_uvm
      Then, unload nvidia

      sudo rmmod nvidia
      Troubleshooting
      If you get an error like rmmod: ERROR: Module nvidia is in use, which indicates that the kernel module is in use, you should kill the process that using the kmod:

      sudo lsof /dev/nvidia*
      and then kill those process, then continue to unload the kmods.

      Test
      Confirm you successfully unload those kmods

      lsmod | grep nvidia
      You should get nothing. Then confirm you can load the correct driver:

      nvidia-smi
      You should get the correct output.

    • A

      ONT basecalling Guppy
      • anneng

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      A

      查询流程配置
      guppy_basecaller --print_workflows

      R10版本:
      sudo guppy_basecaller -i ./fast5 -s ./fastq -c dna_r10.3_450bps_hac.cfg --num_callers 2 --cpu_threads_per_caller 1 --gpu_runners_per_device 20 --device "auto"

    • A

      常用生物学软件
      • anneng

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      A

      https://bioedit.software.informer.com/7.2/
      bioedit

    • A

      Nodebb论坛安装过程记录
      • anneng

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      I

      @ice-melt

      另外还有论坛网页经常显示连接已断开的问题,
      解决方法:
      将 nodebb论坛的config.json中的 url 修改的和 nginx 的一致
      example:

      cat /etc/nginx/sites-enabled/nodebb ... server_name an.forum.genostack.com; ... cat /path/to/nodebb/config.json ... "url": "http://an.forum.genostack.com", ...
    • A

      NGS常见术语
      • anneng

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      A

      https://www.biostars.org/p/43897/
      Read group的含义

    • A

      三代测序数据分析
      • anneng

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      A

      alignment (Minimap2), variant calling with various tools (Clair, Longshot and Sniffles), and methylation calling (Nanopolish).

    • A

      fastq的质控工具 fastqc
      • anneng

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      I

      补充:fastqc报告各模块原始说明文档链接

      http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3 Analysis Modules

    • A

      宏基因组
      • anneng

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    • A

      病原体检测
      • anneng

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      A

      https://www.pathogenomix.com/

    • A

      疾病数据库
      • anneng

      1
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      6
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