This pipeline is built for the assembly of long reads using a specified set of three arguments and dependecies. it utilize long read data for genome assembly and short read data for genome size estimation, incorporating quality assesement using R script.

Pipeline overview:

workflow of the pipeline is as follow:

1. Raw Reads statistics

2. Genome size estimation using short reads

3. De novo genome assembly

4. Quality assesement of genome assembly using N50 statistics and BUSCO

Pipeline usage:

To run the pipeline, execute the main script with following argument:

1$ = path to Long Read folder data/raw/*.fastq

2$ = path to Short Read folder

3$ = specify BUSCO lineage lactobacillales_odb10

Pipeline dependencies:

N50_reads.R for generating length read distribution

N50_contigs.R for performing quality assesement of N50