diff --git a/generation.sh b/generation.sh
index fa6ae17..7586615 100755
--- a/generation.sh
+++ b/generation.sh
@@ -19,5 +19,5 @@ fastq=".fastq"
 filename="sequence"
 prefix="curesim_"
 
-Rscript src/repertoire.r "$sequences" && java -jar tools/CuReSim.jar -n "$sequencing_runs" -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$filename$fasta" -o "$data_directory$prefix$filename$fastq"
+Rscript src/repertoire.r "$sequences" "$sequencing_runs" && java -jar tools/CuReSim.jar -n "$sequencing_runs" -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$filename$fasta" -o "$data_directory$prefix$filename$fastq"
 rm "$data_directory/log.txt"
diff --git a/src/repertoire.r b/src/repertoire.r
index 60c03c3..c8107e6 100644
--- a/src/repertoire.r
+++ b/src/repertoire.r
@@ -10,13 +10,14 @@ generate_repertoire <- function(number_of_sequences) {
   ))
 }
 
-save_data <- function(data) {
+save_data <- function(data, reads) {
   Biostrings::writeXStringSet(data$sequence, "data/sequence.fasta")
   vdj_sequences <- data[-1]
-  write.csv(vdj_sequences, "data/vdj_alignment.csv", row.names = FALSE)
+  amplified_vdj <- vdj_sequences[rep(seq_len(nrow(vdj_sequences)), reads), ]
+  write.csv(amplified_vdj, "data/vdj_alignment.csv", row.names = FALSE)
 }
 
-process_data <- function(repertoire) {
+process_data <- function(repertoire, reads) {
   columns <- c(
     "sequence", "v_sequence_alignment",
     "d_sequence_alignment", "j_sequence_alignment"
@@ -24,17 +25,17 @@ process_data <- function(repertoire) {
   data <- repertoire[, columns]
   dna_sequence <- Biostrings::DNAStringSet(data$sequence)
   data$sequence <- Biostrings::reverseComplement(dna_sequence)
-  save_data(data)
+  save_data(data, reads)
 }
 
 parse_cli_arguments <- function() {
   args <- commandArgs(trailingOnly = TRUE)
-  if (length(args) != 1) {
-    stop("usage: repertoire.r <number of sequences>")
+  if (length(args) != 2) {
+    stop("usage: repertoire.r <number of sequences> <sequencing runs>")
   }
-  return(args[1])
+  return(c(args[1], args[2]))
 }
 
 args <- parse_cli_arguments()
 repertoire <- generate_repertoire(number_of_sequences = as.integer(args[1]))
-process_data(repertoire)
\ No newline at end of file
+process_data(repertoire = repertoire, reads = as.integer(args[2]))
\ No newline at end of file