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#!/bin/bash

# Download the paired end reads for B thuringiensis
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR209/001/SRR2093871/SRR2093871_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR209/001/SRR2093871/SRR2093871_2.fastq.gz

# Run FastQC to check data for error
fastqc SRR2093871_1.fastq.gz  
fastqc SRR2093871_2.fastq.gz 

# fastqc should indicate no problems - move on to assembly
cd ../
mkdir 01_spades
cd 01_spades

# Run spades with four threads and the pair-end reads (use half your total threads available)

spades.py \
-k 21,33,55,77,99,127 \ # list of k-mer sizes
-t 4 \ # set number of threads
--pe1-1 ../00_rawdata/SRR2093871_1.fastq.gz \ # file with left reads for paired-end library 
--pe1-2 ../00_rawdata/SRR2093871_2.fastq.gz \ # file tith right reads for paired-end library 
--careful \ # reduce number of mismatches and short indels
-o assembly # output directory is assembly

# Now let's use quast to test our scaffolds

./quast.py -t 4 ~/BIFS619/Bthuringiensis/01_spades/assembly/scaffolds.fasta

# Examine the results:
cd quast_results/latest/
firefox report.html