=============================================

Input data:
	paired end data:
		first read pair: <LEFT.fq>
		second read pair: <RIGHT.fq>

=============================================

Assembling reads:

I. Quality control
	commands 
		1) first read pair: programs/FastQC/./fastqc -o qc_<LEFT.fq> -f fastq <LEFT.fq>
		2) second read pair: programs/FastQC/./fastqc -o qc_<RIGHT.fq> -f fastq <RIGHT.fq>


II. Assembling reads to genome

	velvet: 1) programs/velvet_1.2.10/./velveth velvet_assembly_31 31 -fastq -shortPaired1 <LEFT.fq> -shortPaired2 <RIGHT.fq>
		2) programs/velvet_1.2.10/./velvetg velvet_assembly_31

	spades:
		python programs/SPAdes-3.9.0-Linux/bin/spades.py -o spades_assembly -1 <LEFT.fq> -2 <RIGHT.fq> --careful -t 4 -m 4


	Rename assembled genome: mv <assembled_genome.fa> <your_name_program_reads.fa>
		eg. mv spades_assembly/scaffolds.fasta spades_assembly/lorinc_spades_helico_reads.fa

III. Comparing genome assemblies (when one or more assembled genomes are avaliable)
	Quast: python programs/quast-4.3/quast.py -o comparison <input1.fa> <input2.fa> .. <inputN.fa>

	eg. python programs/quast-4.3/quast.py -o comparison velvet/contigs.fa spades_assembly/scaffolds.fasta spades_assembly_perfect/scaffolds.fasta reference/Helico_N1_uniform.fna

IV. Comparing genome alignments using dotblots:
	Start GUI of Gepard (java jar file in programs: Gepard-1.40.jar)