Whole genome sequencing, Amblyseius swirskii pooled population, ONT MinION -- ONT data I2 run 1 part II fast5

ReadMe: ONT data I2 runKim Ferguson, [e-mail] or [e-mail] University and Research<br>This ReadMe file is for all files associated with this project, and is present in each data package.<br>There are five .tar file sets in total available on figshare:&gt; 20171130_1637_FAH35464_I2_run 1 part I fast5.tar&gt; 20171130_1637_FAH35464_I2_run 1 part II fast5.tar&gt; 20171201_0934_FAH35464_I2_run 1 restart 1 fast5.tar&gt; 20171201_0954_FAH35464_I2_run 1 restart 2 nobasecalling fast5.tar&gt; ONT data I2 run fastq.tar<br>Read creation dates: 30-11-2017 and 01-12-2017Albacore run date: 04-12-2017<br>Organism: Amblyseius swirskiiPopulation: Koppert biocontrol population, inbred for 10 generationsCollected: &gt;1000 individuals for DNA extraction, males, females, juveniles, placed in 96% EtOHContamination: Collected with food source, pollen from Typha latifolia, and likely was part of DNA extractionExtraction protocol: QIAGEN MagAttract HMW DNA Kit (QIAGEN) according to the manual, while the final DNA product was eluted with nuclease free waterSequenced using ONT MinION sequencing technology<br>MinION model: MinION Mk1BFlowcell: FAH35464 FLO-MIN107 R9.5Ligation kit: Ligation Sequencing Kit version 108 (SQK-LSK108) (no genomic shearing)MinKNOW: version 1.10.16Reads that were basecalled in the cloud: &gt; /20171130_1635_FAH35464_I2_run 1 mux&gt; /20171130_1635_FAH35464_I2_run 1 full&gt; /20171130_1635_FAH35464_I2_run 1 restart 1 mux&gt; /20171130_1635_FAH35464_I2_run 1 restart 1 fullReads that were basecalled using Albacore (version 2.1.3):&gt; /20171201_0952_FAH35464_I2_run 1 restart 2 nobasecalling mux&gt; /20171201_0954_FAH35464_I2_run 1 restart 2 nobasecalling fullAlbacore results:&gt; /basecalled_reads 20171201_0952_FAH35464_I2_run 1 restart 3 nobasecalling mux&gt; /basecalled_reads 20171201_0954_FAH35464_I2_run 1 restart 3 nobasecalling full<br>Data further used in Paspati et al, in prep<br>Fun facts:<br>Files have been separated into fast5 and fastq files, with additional splitting into parts I and II for "/20171130_1635_FAH35464_I2_run 1 full" due to size. Each fast5 folder has been uploaded separateley<br>fast5 folders are often separated into Fail, Pass, and Skip, this is related to the cloud basecalling by the MinKNOW program, based on initial and ongoing quality assessments.<br>fastq folders and files would be considered raw and uncorrected, and were either basecalled in th cloud or using Albacore (see below). All fastq folders have been compressed and uploaded together.<br>There are two restarts in this sequencing run, due to MinKNOW crashing, either after a few hours or overnight. After the second crash, we decided to switch to no basecalling in hope that this would solve the issues.

# 自述文件：ONT（Oxford Nanopore Technologies）I2测序运行数据
作者：Kim Ferguson，邮箱：[e-mail] 或 [e-mail]
瓦赫宁根大学及研究中心

本自述文件对应本项目的全部关联文件，且每个数据包中均包含该文件。

figshare平台共提供5组.tar格式文件集，具体如下：
> 20171130_1637_FAH35464_I2_run 1 part I fast5.tar
> 20171130_1637_FAH35464_I2_run 1 part II fast5.tar
> 20171201_0934_FAH35464_I2_run 1 restart 1 fast5.tar
> 20171201_0954_FAH35464_I2_run 1 restart 2 nobasecalling fast5.tar
> ONT data I2 run fastq.tar

数据创建日期：2017年11月30日及2017年12月1日
Albacore（碱基识别软件）运行日期：2017年12月4日

生物种：斯氏钝绥螨（Amblyseius swirskii）
种群来源：科伯特生防种群，经10代近交培育
样本采集：选取超1000个个体用于DNA提取，涵盖雄虫、雌虫及若虫，置于96%乙醇中保存
污染情况：样本采集时带有食物源——香蒲（Typha latifolia）花粉，且该花粉可能混入DNA提取流程
DNA提取流程：采用QIAGEN MagAttract 高分子量DNA提取试剂盒（QIAGEN MagAttract HMW DNA Kit），严格遵循试剂盒说明书操作，最终使用无核酸酶水洗脱得到DNA产物

测序采用ONT MinION测序技术：
MinION型号：MinION Mk1B
测序流通池：FAH35464 FLO-MIN107 R9.5
连接试剂盒：连接测序试剂盒版本108（SQK-LSK108），未进行基因组片段剪切
MinKNOW测序控制软件版本：1.10.16

云端碱基识别的测序读段（reads）数据：
> /20171130_1635_FAH35464_I2_run 1 mux
> /20171130_1635_FAH35464_I2_run 1 full
> /20171130_1635_FAH35464_I2_run 1 restart 1 mux
> /20171130_1635_FAH35464_I2_run 1 restart 1 full

使用Albacore（版本2.1.3）进行碱基识别的测序读段数据：
> /20171201_0952_FAH35464_I2_run 1 restart 2 nobasecalling mux
> /20171201_0954_FAH35464_I2_run 1 restart 2 nobasecalling full

Albacore碱基识别结果：
> /basecalled_reads 20171201_0952_FAH35464_I2_run 1 restart 3 nobasecalling mux
> /basecalled_reads 20171201_0954_FAH35464_I2_run 1 restart 3 nobasecalling full

本数据集将用于Paspati等学者的待发表研究中。

## 趣味补充
文件已按fast5格式与fastq格式分类存储；针对`/20171130_1635_FAH35464_I2_run 1 full`数据集，因文件体积过大已拆分为第一、第二部分，每个fast5文件夹均单独上传。
fast5文件夹通常分为Fail、Pass与Skip三类，该分类与MinKNOW软件基于初始及持续质量评估开展的云端碱基识别流程相关。
fastq文件夹及文件属于原始未校正测序数据，可分为云端碱基识别及Albacore软件碱基识别两类（详见上文），所有fastq文件夹均经压缩后合并上传。
本次测序运行共出现两次重启：因MinKNOW软件崩溃所致，分别发生在运行数小时后及过夜运行后；第二次崩溃后，我们尝试关闭碱基识别功能以解决该问题。