myonaung / naung-et-al-2021

Bioinformatics Pipeline for MalariaGen's Pf3k and MalariaGen Community (PNG) WGS analysis which is used to characterise diversity analysis of vaccine candidate antigens

Pf3K PNG WGS Scripts

1. Data_preprocessing.pdf contains steps for hard-filtering, pre-processing of GATK outputs.
2. ./Phasing_Haplotype/ folder contains R scripts used in phasing haplotype and generating FastA files.
3. ./Scripts/ folder contrains miscellaneous scripts used in cleaning FastA files
4. ./Raw_FASTA/ folder contrains sequences used in the manuscripts
5. ./common_haplotype/ folder contains fasta sequences of the first 10 most common haplotypes for each antigen with H1 being the most common and H10 being the 10th most common haplotype - complementary to table S2.

Acknowledgment: We would like to thank Stuart Lee (Bahlo Lab) for the help and guidance for hard-filtering, pre-processing of GATK outputs.