Overview of bioinformatic pipeline - RebeccaJSmith89/SABT_bioinformatics GitHub Wiki

  • make reference sequences and create a fastq file
  • Align reads to reference sequence using ...(one of these) BWA, Bowtie2
    • these create BAM files
  • Convert BAM to SAM files using samtools *samtools may require downloading java first *Create a loop to do this for all reads *first try on your own computer, then scale up to run all on Rocky *Call SNPs using GATK