data_generation_commands.md

Data generation

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Sources:

• Reference genome
• Available sample genome reads

Tools used:

• bwa
• samtools
• freebayes
• edso

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Get the vcf file

Index the reference genome
bwa index genome_assemblies_genome_fasta.tar

Align and index every read (example with read SRR10058833)
bwa mem reference_genome.fna SRR10058833_1.fastq.gz SRR10058833_2.fastq.gz -R '@RG\tID:SRR10058833\tSM:SRR10058833\tPL:illumina\tLB:SRR10058833\tPU:unit' | samtools view -S -b - | samtools sort -o SRR10058833.bam ; samtools index SRR10058833.bam

Create vcf file from the samples specified in bam_list.txt (bam_list.txt: line separated sample_i.bam)
freebayes -f reference_genome.fna -L bam_list.txt > sample_i.vcf

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Get the bubble graph

./edso reference_genome.fna variants.vcf outfile.eds