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 ResearchThis ReadMe file is for all files associated with this project, and is present in each data package.There are five .tar file sets in total available on figshare:> 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.tarRead creation dates: 30-11-2017 and 01-12-2017Albacore run date: 04-12-2017Organism: Amblyseius swirskiiPopulation: Koppert biocontrol population, inbred for 10 generationsCollected: >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 technologyMinION 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: > /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 fullReads that were basecalled using Albacore (version 2.1.3):> /20171201_0952_FAH35464_I2_run 1 restart 2 nobasecalling mux> /20171201_0954_FAH35464_I2_run 1 restart 2 nobasecalling fullAlbacore results:> /basecalled_reads 20171201_0952_FAH35464_I2_run 1 restart 3 nobasecalling mux> /basecalled_reads 20171201_0954_FAH35464_I2_run 1 restart 3 nobasecalling fullData further used in Paspati et al, in prepFun facts: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 separateleyfast5 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.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.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.

# 说明文档：ONT I2 run测序数据集
作者：Kim Ferguson，邮箱：[e-mail] 或 [e-mail]
瓦赫宁根大学及研究中心（Wageningen University and Research）
本说明文档适配本项目的全部关联文件，且已随每个数据数据包一并提供。

本数据集在figshare平台共提供5个.tar压缩包集合，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

数据文件创建日期：2017年11月30日、2017年12月1日
Albacore（碱基调用软件）运行日期：2017年12月4日

实验物种：智利小植绥螨（Amblyseius swirskii）
种群来源：Koppert生物防治种群，经10代近交培育

样本采集：采集超过1000头个体用于DNA提取，涵盖雄虫、雌虫及幼体，样本置于96%乙醇中保存

样本污染说明：采集时附带了食物来源——宽叶香蒲（Typha latifolia）花粉，该成分大概率也被纳入了DNA提取流程

DNA提取方案：严格按照说明书使用凯杰（QIAGEN）MagAttract高分子量DNA提取试剂盒进行操作，最终DNA产物以无核酸酶水洗脱

测序平台：采用牛津纳米孔测序技术（Oxford Nanopore Technologies, ONT）MinION纳米孔测序平台
测序仪型号：MinION Mk1B
流动槽编号：FAH35464 FLO-MIN107 R9.5
建库连接试剂盒：连接测序试剂盒V108（SQK-LSK108），未进行基因组片段剪切操作
测序控制软件：MinKNOW 版本1.10.16

云端碱基调用的reads数据路径：
> /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）进行碱基调用的reads数据路径：
> /20171201_0952_FAH35464_I2_run 1 restart 2 nobasecalling mux
> /20171201_0954_FAH35464_I2_run 1 restart 2 nobasecalling full

Albacore碱基调用结果路径：
> /basecalled_reads 20171201_0952_FAH35464_I2_run 1 restart 3 nobasecalling mux
> /basecalled_reads 20171201_0954_FAH35464_I2_run 1 restart 3 nobasecalling full

本数据集后续将用于Paspati等人的待发表研究

附注：
1. 本数据集按fast5与fastq格式进行分类存储；其中路径为"/20171130_1635_FAH35464_I2_run 1 full"的文件因体积过大，被拆分为第一、第二两个子部分。每个fast5文件夹均单独上传。
2. fast5文件夹通常会按照MinKNOW软件的云端碱基调用质量评估结果，进一步划分为Fail（失败）、Pass（通过）与Skip（跳过）三类。
3. fastq格式的文件夹与文件均为未校正的原始数据，其碱基调用方式分为云端调用与Albacore软件调用两种（详见前文）。所有fastq格式文件夹均经压缩后统一上传。
4. 本次测序运行共发生两次重启，原因为MinKNOW软件崩溃：第一次崩溃发生在运行数小时后，第二次则在隔夜运行期间。第二次崩溃后，我们决定切换至无碱基调用模式，以期解决软件崩溃问题。