Re-sequencing of Foc isolates representing races to understand the pathogenicity mechanism
Total 56 isolates of Foc representing different races and locations in India where chickpea is grown has been used for the re-sequencing study. Raw data was subjected to filtration and correction steps using Trimmomatic v0.33, to reduce sequencing errors and get high quality data. The high quality reads obtained were aligned to Foc reference sequence (unpublished) using Bowtie2 v2.2.4 with default parameters. The alignment results in form of bam files were then used to calculate various alignment statistics like depth, coverage etc. Samples with lower alignment percentage (≤ 75%) were removed from analysis. Further, these bam files were adjusted for PCR duplicates and improved using Picard tools v1.119 and GATK v3.3. Further analysis is in progress.