从NGS中检测新的病原体在测序过程中实时读取。
deepaclive的Python项目详细描述
DeePaC现场
用于实时分析Illumina测序运行的DeePaC插件。捕获HiLive2输出并使用深层神经网络 直接从不良反应检测新的病原体。在
我们建议您看看：
- 在
DeePaC主回购：https://gitlab.com/rki_bioinformatics/DeePaC
- 教程
- 经过训练的内置模型
- 用于原始模型和deepac live模型的数据集
- 规范和文件
- 在
HiLive2回购：https://gitlab.com/rki_bioinformatics/HiLive2。在
- 广泛的教程
- 规范和文件
安装
# Optional, but recommended: for GPU users
conda install tensorflow-gpu
# Install deepac-live
conda install -c bioconda deepac-live
# Optional: viral built-in models
conda install -c bioconda deepacvir
或者，也可以使用pip：
^{pr2}$基本用途
# Run locally: build-in model for bacteria
deepac-live local -c deepac -m rapid -s 25,50,75,100,133,158,183,208 -l 100 -i hilive-out -o temp -I temp -O output -B ACAG-TCGA,undetermined
# Run locally: build-in model for viruses
deepac-live local -c deepacvir -m rapid -s 25,50,75,100,133,158,183,208 -l 100 -i hilive-out -o temp -I temp -O output -B ACAG-TCGA,undetermined
# Run locally: custom model
deepac-live local -C -m custom_model.h5 -s 25,50,75,100,133,158,183,208 -l 100 -i hilive-out -o temp -I temp -O output -B ACAG-TCGA,undetermined
高级用法
设置远程接收器
# Setup sender on the source machine
deepac-live sender -s 25,50,75,100,133,158,183,208 -l 100 -A -i hilive-out -o temp -r user@remote.host:~/rem-temp -k privatekey -B ACAG-TCGA,undetermined
# Setup receiver on the target machine
deepac-live receiver -c deepacvir -m rapid -s 25,50,75,100,133,158,183,208 -l 100 -I rem-temp -O output -B ACAG-TCGA,undetermined
再滤波器：信号群和替代阈值
# Setup an ensemble on the target machine
deepac-live refilter -s 25,50,75,100,133,158,183,208 -l 100 -i rem-temp -I output_1,output_2 -O final_output -B ACAG-TCGA,undetermined
# Use another threshold
deepac-live refilter -s 25,50,75,100,133,158,183,208 -l 100 -i rem-temp -I output_1 -O final_output -t 0.75 -B ACAG-TCGA,undetermined
- 项目
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