Additional file 1: Figure S1. of Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi

Flowchart to determine new putative TcTS sequences. Step 1: The sequences from the 1430 annotated TcTS genes of the current genome plus up to 1Kb flanking sequence on both the 5′ and 3′ ends were BLASTed (BLASTN) against the 1,131,562 wgs sequence reads, resulting in over 257,824 matching reads. Step 2: resulting reads were BLASTed (BLASTN) against the contigs of the current genome to map them to the most homologous location, resulting in nearly 130k reads mapping to contigs containing no annotated genes. The regions were collapsed into 9852 distinct contig regions. Step 3: the resulting contig regions were BLASTed (BLASTX) against the 735 “full length” TcTS genes in the annotated genome to identify TcTS-like sequences, resulting in 2007 candidate TcTS sequences. Step 4: the candidate sequences were BLASTed (BLASTP) against the entire TSKTSC genome to verify that the top hit was a TcTS sequence. Discarding those that were not resulted in 1780 additional TcTS sequences. (TIF 2089 kb