diff --git a/src/alignment.r b/src/alignment.r
new file mode 100644
index 0000000..ea6d966
--- /dev/null
+++ b/src/alignment.r
@@ -0,0 +1,17 @@
+library(Biostrings)
+library(fastqcr)
+
+parse_data <- function(files) {
+  reversed_sequences <- Biostrings::readQualityScaledDNAStringSet(files[1])
+  sequences <- Biostrings::reverseComplement(reversed_sequences)
+  vdj_alignment <- read.csv(files[2])
+  vdj_string_set <- lapply(vdj_alignment, FUN = Biostrings::DNAStringSet)
+  return(list(sequences, vdj_string_set))
+}
+
+align_sequences <- function(sequences, vdj_segments) {
+
+}
+
+input_files <- c("data/curesim_sequence.fastq", "data/vdj_alignment.csv")
+data <- parse_data(input_files)
\ No newline at end of file