Bioinformatics Codes

Here are some basic codes and pipelines used extensively in bioinformatics. Given below is a brief description for each of the provided codes.

1. SNP_Calling.sh: This code takes FASTQ reads and a reference genome as an input. It aligns the FASTQ reads to the reference genome to create an alignment file. It then processes the alignment file followed by variant calling. This pipeline employs GATK (Genome Analysis Toolkit- https://gatk.broadinstitute.org/hc/en-us) for this.
2. needleman_wunsch.py: The Needleman-Wunsch Alogirthm is a popular algorithm used to align protein or nucleotide sequences using Global Alignment. This code has been developed without importing numpy and is an easy to understand approach for biologists new to coding!
3. smith_watermann.py: Smith-Watermann Algorithm is a popular algorithm used to align protein or nucleotide sequences using Local Alignment. This code has been developed without importing numpy and is an easy to understand approach for biologists new to coding!