Sri Lankan Leishmania donovani causing cutaneous leishmaniasis
Genomic DNA was sheared into fragments of 100–1,200 bp (Nebulizer, Illumina) and was made into a paired-end DNA sequencing (DNA-seq) library using the Genomic DNA Sample Preparation Kit (Illumina, San Diego, USA). Libraries were sequenced using the Genome Analyzer IIx (Illumina). Reads were aligned against the reference genome (L. donovani BPK282/Ocl4, cloned line from Nepal). Somy and copy number information for each chromosome  were calculated independently using in-house built perl scripts (see supplementary methods). Single nucleotide polymorphism and small indels were called by inputting alignment files (bam) from all the four libraries into GATK software. A thorough manual inspection revealed around 30% of variant calls were false positives or incorrectly genotyped. Calls were then validated manually and reassigned genotypes if necessary. All the validated variants that were consistent within each group (VL and CL) but different between them were then analyzed in detail to study the effects on protein coding genes using snpEFF(v3.2) tool.