Resequence_Data_Processing

#Trimmomatic.sh was used to trim the resequencing data to the following specifications: #Remove adapters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10) #Remove leading low quality or N bases (below quality 3) (LEADING:3) #Remove trailing low quality or N bases (below quality 3) (TRAILING:3) #Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 20 (SLIDINGWINDOW:4:20) #Drop reads below the 50 bases long (MINLEN:50)