Amblyseius swirskii I2 ONT Minion Raw and Uncorrected Data

ReadMe: ONT data I2 run

Kim Ferguson, kim.ferguson@wur.nl or kfergy@gmail.com

Wageningen University and Research

This 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.tar

Read creation dates: 30-11-2017 and 01-12-2017

Albacore run date: 04-12-2017

Organism: Amblyseius swirskii

Population: Koppert biocontrol population, inbred for 10 generations

Collected: >1000 individuals for DNA extraction, males, females, juveniles, placed in 96% EtOH

Contamination: Collected with food source, pollen from Typha latifolia, and likely was part of DNA extraction

Extraction protocol: QIAGEN MagAttract HMW DNA Kit (QIAGEN) according to the manual, while the final DNA product was eluted with nuclease free water

Sequenced using ONT MinION sequencing technology

MinION model: MinION Mk1B

Flowcell: FAH35464 FLO-MIN107 R9.5

Ligation kit: Ligation Sequencing Kit version 108 (SQK-LSK108) (no genomic shearing)

MinKNOW: version 1.10.16

Reads 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 full

Reads 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 full

Albacore results:

> /basecalled_reads 20171201_0952_FAH35464_I2_run 1 restart 3 nobasecalling mux

> /basecalled_reads 20171201_0954_FAH35464_I2_run 1 restart 3 nobasecalling full

Data further used in Paspati et al, in prep

Fun 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 separateley

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.

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.