FuzzySequencer

Code for A fuzzy sequencer for rapid DNA fragment counting and genotyping

Required softwares

Software	Tested version
BWA	0.7.12-r1039
Samtools	1.10
Python	3.7.7

Files

• genome/lambda_phage.fasta: Reference genome sequence of lambda phage downloaded from: https://www.ncbi.nlm.nih.gov/nuccore/NC_001416.1
• genome/bMK.fasta: The BitSeq version of lambda phage genome (MK mode).
• genome/bRY.fasta: The BitSeq version of lambda phage genome (RY mode).
• data/fasta: Simulated sequencing reads of lambda phage genomic DNA. It is simulated that the same 100 DNA molecules are sequenced by all three sequencing methods: the conventional 4-base sequencing, BitSeq in MK mode, and BitSeq in RY mode. The header of each read is their starting sites on the genome.
• data/sam: Mapping results of the simulated sequencing reads in the SAM format.
• genome_encoding.py: The code that encode lambda phage genome into BitSeq formats.
• build_genome_index.sh: Build index for the three FASTA files in the genome folder using BWA.
• mapping.sh: Map the simulated sequencing reads, including BitSeq reads, to their corresponding genomes.

How to run the demo

1. Run genome_encoding.py and it will encode genome/lambda_phage.fasta into genome/bMK.fasta and genome/bRY.fasta (already provided in the directory).
2. Run build_genome_index.sh and it will build the genome index for the three fasta files in the genome directory (already provided in the directory).
3. Run mapping.sh and it will map the simulated sequencing reads in the data/fasta directory to their corresponding genomes. The resulting SAM files are already provided in the data/sam directory. From the SAM files we can see that they are all mapped to the sites where they originated.