Skip to content

Latest commit

 

History

History
67 lines (48 loc) · 2.57 KB

README.md

File metadata and controls

67 lines (48 loc) · 2.57 KB
Raw

Medaka

Description

This directory archives the pipelines for Medaka polishing and Yak based polished assembly QV evaluation.

Execution environments

  1. Medaka environment is provided in medaka.yaml. To recreate this environment run
conda env create -f medaka.yaml;
  1. Yak environment is provided in yak.yaml. To recreate this environment run
conda env create -f yak.yaml;

Pipeline

  1. Make sure you have run the pipeline in ../../flye/scripts/README.md and ../../yak/scripts/README.md.

To run Flye genome assembly please follow the instruction in here.

The genome draft used for Medaka polishing is based on Flye assembled contigs.. The evaluation is performed using yak with short-read NGS data.

  1. Run Medaka polishing for R9G4FAST, R9G4HAC, R9G6FAST, R9G6HAC, R9G6SUP, R10D0HAC, and R10D0SUP data bash run_medaka_polishing.sh;

  2. Run yak evaluation for polished data bash cal_polished_yakQV.sh;

Medaka models

The correct Medaka models for different flowcell and basecaller versions of HG002 data is listed below.

Flowcell Basecaller Mode Correct Medaka config
R9 Guppy4.2.2 FAST r941_prom_fast_g303
R9 Guppy4.2.2 HAC r941_prom_high_g4011
R9 Guppy6.3.8 FAST r941_prom_fast_g507
R9 Guppy6.3.8 HAC r941_prom_hac_g507
R9 Guppy6.3.8 SUP r941_prom_sup_g507
R10 Dorado0.4.3 HAC r1041_e82_400bps_hac_v4.1.0
R10 Dorado0.4.3 SUP r1041_e82_400bps_sup_v4.1.0

Result descriptions

  1. Naming pattern For example, R9G4FAST_R9G4HAC means R9G4FAST basecalled FASTQ data using Medaka model for R9G4HAC.

  2. Polished QV shift will be in ./QVshift.csv, the description of each column is as follow:

Column index Column name Column description
1 basecalled The basecalling configuration for the input FASTQ
2 polished contig Medaka model used for genome polishing
3 draft QV Yak QV score of the Flye-assembled draft ($\text{Draft QV}$)
4 polished QV Yak QV score of the polished contig ($\text{Polished QV}$)
5 QV shift $\text{QV shift} = \text{Polished QV} - \text{Draft QV}$

Repeat our results

To repeat our results, please install the aforementioned conda environment first and make sure you have run the pipeline in ../../flye/scripts/README.md and ../../yak/scripts/README.md, then run

bash ./run_all.sh;

Note that, Medaka is relatively slow. We finished all 49 groups of polishing with 32 cores and an Nvidia RTX A5000 in 3 weeks.