pageneck / dna-sequencing-fa-fastq-python

DNA Sequencing Analysis: lambda_virus.fa and Human Genome FASTQ file with Python

Genome Data

• lambda virus genome, at https://d28rh4a8wq0iu5.cloudfront.net/ads1/data/lambda_virus.fa

• real DNA sequencing reads derived from a human https://d28rh4a8wq0iu5.cloudfront.net/ads1/data/ERR037900_1.first1000.fastq

SOURCE: Ajay, S. S., Parker, S. C., Abaan, H. O., Fajardo, K. V. F., & Margulies, E. H. (2011). Accurate and comprehensive sequencing of personal genomes. Genome research, 21(9), 1498-1505.

Algorithms Implmented

• Naive exact matching algorithm that is strand-aware. That is, instead of looking only for occurrences of P in T, additionally look for occurrences of the reverse complement of P in T

• Naive matching algirithm that allows up to 2 mismatches per occurrence.