Program, Pipeline Name or Method Name

nanoplot, downpore, flye, racon, medaka

Program, Pipeline or Method version

Version 1

Source Name

HalFul_medaka.FINAL.fasta

Time Executed

June 23, 2021, midnight

Category

Genome structure

Description

## QC The quality of the nanopore reads was determined using NanoPlot (1.31.0) and trimmed using downpore (0.3.3--h375a9b1_0). ## Genome Assembly Flye Version 2.8-b1674 was used to assemble the nanopore data for each sample using the following parameters (--nano-raw --genome-size 1800m --threads 20 -i 4). These parameters assume a genome size of 1800, raw nanopore reads as input and 4 rounds of flye long read polishing. ## Genome Polishing using Racon and Medaka The assembly output from Flye was first polished using Racon (1.4.13--he513fc3_0) one time with the following parameters (-m 8 -x -6 -g -8 -w 500) as recommended for input to Medaka. Medaka (2.17-r941) was then run on the Racon output one time using the default parameters and the r941_min_high_g303_model.hdf5 model to produced the polished assembly.

File

halful_medaka.final_.fasta