研究者先是测试了ONT旗下四款碱基识别程序——Albacore、Guppy、Scrappie和Flappie并运行和R9.4reads配套的所有可用版本,另外还测试了一款仍处于研发状态的、基于深度神经网络算法的碱基识别软件Chiron等。 接下来是进行自定义模式模拟,研究者使用Sloika工具包——一种可生成用于Guppy的模式神经网络模拟工具,模拟的数据来自...
研究者先是测试了ONT旗下四款碱基识别程序——Albacore、Guppy、Scrappie和Flappie并运行和R9.4reads配套的所有可用版本,另外还测试了一款仍处于研发状态的、基于深度神经网络算法的碱基识别软件Chiron等。 接下来是进行自定义模式模拟,研究者使用Sloika工具包——一种可生成用于Guppy的模式神经网络模拟工具,模拟的数据来自...
ONT guppy mirror 能饮一杯吴先生 生物信息学界的一枚小学生 GPU version https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy…阅读全文 赞同2 6 条评论 分享收藏 有哪些生物信息学工具可以对已公开的个体基因组测序结果(如Watson的和Venter的)进行全面比较? Xi Yang 知乎说...
GPU version https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy_6.0.1_linux64.tar.gz CPU version https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy-cpu-6.1.5-1.el7.x86_64.rpm Install Guppy using dpkg:: alien ont-guppy-cpu-6.1.5-1.el7.x86_64.rpm dpkg -i ont...
GPU version (experimental, not advised to use) There is also GPU version of basecaller, which is slightly worse and slower than guppy, butdoes notrequire compute capability 6.2 (anything which can run Pytorch 1.0 is good enough). If you want to use GPU version, we recommend setting up Con...
The latest update removes previous basecalls and replaces them with basecalls obtained from a development version of the GPU accelerated guppy basecaller. This basecaller contains several advances and fixes to that used previously; hence the removal of the previous calls. The alignments provided ...
ONT. The bases were called using Guppy (versions provided in Table1), under the high-accuracy model in MinIT taking advantage of its GPU. We here only used MinION and Flongle flow cells for barcoding. This preference was based on four considerations: (1) Scaling; i.e., ability to ...
Adds version checking for MinKNOW and Guppy/Dorado, logs if not compatibile(#351) 2024.1.0 bug fix type for--wait-on-readytype and actual function(#327),(#323) mutiple suffix.mmisupport(#330) Change the defaultunblock_durationon theAnalysisclass to useDEFAULT_UNBLOCKvalue defined in_cli_arg...
There is also GPU version of basecaller, which is slightly worse and slower than guppy, but does not require compute capability 6.2 (anything which can run Pytorch 1.0 is good enough). If you want to use GPU version, we recommend setting up Conda environment with pytorch first. It can be...
表现与Albacore相当,不过最新版本Guppy v2.2.3在默认模式下的read精确度(Q8.9)上不如一致性准确度(Q22.8)。在使用flip-flop模式时,一致性准确度相当(Q23.0),但read精确度更佳(Q9.7)。相较其他软件,其在GPU加持下运行速度最快(约1500000bp/s) ③Scrappie和Flappie ...