amandajoelle/Trimming_Awendungen_fuer_-die-_Qualitaetsverbesserung_von_Nanoporez_Sequenzierungsdaten

nextflow-test

Pipeline to analyse and make a data quality control of an RNA-Genom using two different assembler frameworks

First Step

Install Conda

https://linuxhint.com/install-anaconda-ubuntu-22-04/ 

Install Prinseq, Flye, Quast.

Configure conda

 conda config –add channels bioconda   conda config –add channels conda-forge   conda config –show channels  

Install Priseq

$ wget -N http://downloads.sourceforge.net/project/prinseq/standalone/prinseq-lite-0.20.4.tar.gz

$ tar -zxvf prinseq-lite-0.20.4.tar.gz

$ cp -puv prinseq-lite-0.20.4/prinseq-lite.pl /usr/local/bin/prinseq-lite && chmod +x /usr/local/bin/prinseq-lite

$ cp -puv prinseq-lite-0.20.4/prinseq-graphs.pl /usr/local/bin/prinseq-graphs && chmod +x /usr/local/bin/prinseq-graphs

Install Flye and Quast

 conda create –n genome_assembly flye  quast  

Activate the environment

 conda env list 

conda activate genome_assembly 

Use

- Prinseq 

 prinseq-lite -fastq .<fastq | fastq.gz> -out_format 1 

EXAMPLE : prinseq-lite.pl -fastq 1_control_psbA3_2019_minq7.fastq -out_format 1

  - Flye 

 flye --nano-raw . -o assembly –g 5.6m -t 10 –i 2 

EXAMPLE :

flye --pacbio-raw 1_control_psbA3_2019_minq7_prinseq_good_OqHZ.fasta --out-dir out_p --threads 4

- Quast 

 quast . . -o 

EXAMPLE : quast -o quast_report E.coli_PacBio_40x.fasta prinseq_good_OqHZ.fasta