diff --git a/src/sickle.h b/src/sickle.h
index e78e667..c697b92 100644
--- a/src/sickle.h
+++ b/src/sickle.h
@@ -98,6 +98,6 @@ typedef struct __cutsites_ {
 /* Function Prototypes */
 int single_main (int argc, char *argv[]);
 int paired_main (int argc, char *argv[]);
-cutsites* sliding_window (kseq_t *fqrec, int qualtype, int length_threshold, int qual_threshold, int no_fiveprime, int trunc_n, int debug);
+cutsites* sliding_window (kseq_t *fqrec, int qualtype, int length_threshold, int qual_threshold, int no_fiveprime, int trunc_n, int drop_n, int debug);
 
 #endif /*SICKLE_H*/
diff --git a/src/sliding.c b/src/sliding.c
index 7573106..5a8193c 100644
--- a/src/sliding.c
+++ b/src/sliding.c
@@ -32,7 +32,7 @@ int get_quality_num (char qualchar, int qualtype, kseq_t *fqrec, int pos) {
 }
 
 
-cutsites* sliding_window (kseq_t *fqrec, int qualtype, int length_threshold, int qual_threshold, int no_fiveprime, int trunc_n, int debug) {
+cutsites* sliding_window (kseq_t *fqrec, int qualtype, int length_threshold, int qual_threshold, int no_fiveprime, int trunc_n, int drop_n, int debug) {
 
 	int window_size = (int) (0.1 * fqrec->seq.l);
 	int i,j;
@@ -112,10 +112,14 @@ cutsites* sliding_window (kseq_t *fqrec, int qualtype, int length_threshold, int
 	}
 
 
-    /* If truncate N option is selected, and sequence has Ns, then */
-    /* change 3' cut site to be the base before the first N */
-    if (trunc_n && ((npos = strstr(fqrec->seq.s, "N")) || (npos = strstr(fqrec->seq.s, "n")))) {
-        three_prime_cut = npos - fqrec->seq.s;
+    /* If truncate N option is selected, and sequence has Ns, then
+     * change 3' cut site to be the base before the first N.
+     * If drop N option is selected, omit the sequence. */
+    if ((npos = strstr(fqrec->seq.s, "N")) || (npos = strstr(fqrec->seq.s, "n"))) {
+        if (trunc_n)
+            three_prime_cut = npos - fqrec->seq.s;
+        else if (drop_n)
+            three_prime_cut = five_prime_cut = -1;
     }
 
     /* if cutting length is less than threshold then return -1 for both */
diff --git a/src/trim_paired.c b/src/trim_paired.c
index 6a42251..2b8f3ad 100644
--- a/src/trim_paired.c
+++ b/src/trim_paired.c
@@ -16,7 +16,7 @@ __KSEQ_READ
 int paired_qual_threshold = 20;
 int paired_length_threshold = 20;
 
-static const char *paired_short_options = "df:r:c:t:o:p:m:M:s:q:l:xng";
+static const char *paired_short_options = "df:r:c:t:o:p:m:M:s:q:l:xnNg";
 static struct option paired_long_options[] = {
     { "qual-type",           required_argument, NULL, 't' },
     { "pe-file1",            required_argument, NULL, 'f' },
@@ -30,6 +30,7 @@ static struct option paired_long_options[] = {
     { "length-threshold",    required_argument, NULL, 'l' },
     { "no-fiveprime",        no_argument,       NULL, 'x' },
     { "truncate-n",          no_argument,       NULL, 'n' },
+    { "drop-n",              no_argument,       NULL, 'N' },
     { "gzip-output",         no_argument,       NULL, 'g' },
     { "output-combo-all",    required_argument, NULL, 'M' },
     { "quiet",               no_argument,       NULL, 'z' },
@@ -95,6 +96,7 @@ void paired_usage (int status, char *msg) {
         "                               trimming. Default %4$d.\n"
         "-x, --no-fiveprime             Don't do five prime trimming.\n"
         "-n, --truncate-n               Truncate sequences at position of first N.\n"
+        "-N, --drop-n                   Discard sequences containing an N.\n"
         "-g, --gzip-output              Output gzipped files.\n"
         "--quiet                        Do not output trimming info\n"
         "--help                         Display this help and exit\n"
@@ -154,6 +156,7 @@ int paired_main(int argc, char *argv[]) {
     int quiet = 0;
     int no_fiveprime = 0;
     int trunc_n = 0;
+    int drop_n = 0;
     int gzip_output = 0;
     int combo_all=0;
     int combo_s=0;
@@ -246,6 +249,10 @@ int paired_main(int argc, char *argv[]) {
             trunc_n = 1;
             break;
 
+        case 'N':
+            drop_n = 1;
+            break;
+
         case 'g':
             gzip_output = 1;
             break;
@@ -276,6 +283,11 @@ int paired_main(int argc, char *argv[]) {
         paired_usage(EXIT_FAILURE, "****Error: Quality type is required.");
     }
 
+    if (trunc_n && drop_n) {
+        fprintf(stderr, "****Error: cannot specify both --truncate-n and --drop-n\n\n");
+        return EXIT_FAILURE;
+    }
+
     /* make sure minimum input filenames are specified */
     if (!infn1 && !infnc) {
         paired_usage(EXIT_FAILURE, "****Error: Must have either -f OR -c argument.");
@@ -414,8 +426,8 @@ int paired_main(int argc, char *argv[]) {
             break;
         }
 
-        p1cut = sliding_window(fqrec1, qualtype, paired_length_threshold, paired_qual_threshold, no_fiveprime, trunc_n, debug);
-        p2cut = sliding_window(fqrec2, qualtype, paired_length_threshold, paired_qual_threshold, no_fiveprime, trunc_n, debug);
+        p1cut = sliding_window(fqrec1, qualtype, paired_length_threshold, paired_qual_threshold, no_fiveprime, trunc_n, drop_n, debug);
+        p2cut = sliding_window(fqrec2, qualtype, paired_length_threshold, paired_qual_threshold, no_fiveprime, trunc_n, drop_n, debug);
         total += 2;
 
         if (debug) printf("p1cut: %d,%d\n", p1cut->five_prime_cut, p1cut->three_prime_cut);
@@ -520,7 +532,7 @@ int paired_main(int argc, char *argv[]) {
     }
 
     if (!quiet) {
-        if (infn1 && infn2) fprintf(stdout, "\nPE forwrd file: %s\nPE reverse file: %s\n", infn1, infn2);
+        if (infn1 && infn2) fprintf(stdout, "\nPE forward file: %s\nPE reverse file: %s\n", infn1, infn2);
         if (infnc) fprintf(stdout, "\nPE interleaved file: %s\n", infnc);
         fprintf(stdout, "\nTotal input FastQ records: %d (%d pairs)\n", total, (total / 2));
         fprintf(stdout, "\nFastQ paired records kept: %d (%d pairs)\n", kept_p, (kept_p / 2));
diff --git a/src/trim_single.c b/src/trim_single.c
index afedd8b..fcdb3d5 100644
--- a/src/trim_single.c
+++ b/src/trim_single.c
@@ -15,7 +15,7 @@ __KSEQ_READ
 int single_qual_threshold = 20;
 int single_length_threshold = 20;
 
-static const char *single_short_options = "df:t:o:q:l:zxng";
+static const char *single_short_options = "df:t:o:q:l:zxnNg";
 static struct option single_long_options[] = {
     { "fastq-file",         required_argument, NULL, 'f' },
     { "output-file",        required_argument, NULL, 'o' },
@@ -53,6 +53,7 @@ void single_usage(int status, char *msg) {
         "                             trimming. Default %4$d.\n"
         "-x, --no-fiveprime           Don't do five prime trimming.\n"
         "-n, --truncate-n             Truncate sequences at position of first N.\n"
+        "-N, --drop-n                 Discard sequences containing an N.\n"
         "-g, --gzip-output            Output gzipped files.\n"
         "--quiet                      Do not output trimming info\n"
         "--help                       Display this help and exit\n"
@@ -92,6 +93,7 @@ int single_main(int argc, char *argv[]) {
     int quiet = 0;
     int no_fiveprime = 0;
     int trunc_n = 0;
+    int drop_n = 0;
     int gzip_output = 0;
     int total=0;
 
@@ -153,6 +155,10 @@ int single_main(int argc, char *argv[]) {
             trunc_n = 1;
             break;
 
+        case 'N':
+            drop_n = 1;
+            break;
+
         case 'g':
             gzip_output = 1;
             break;
@@ -208,12 +214,17 @@ int single_main(int argc, char *argv[]) {
         }
     }
 
+    if (trunc_n && drop_n) {
+        fprintf(stderr, "****Error: cannot specify both --truncate-n and --drop-n\n\n");
+        return EXIT_FAILURE;
+    }
+
 
     fqrec = kseq_init(se);
 
     while ((l = kseq_read(fqrec)) >= 0) {
 
-        p1cut = sliding_window(fqrec, qualtype, single_length_threshold, single_qual_threshold, no_fiveprime, trunc_n, debug);
+        p1cut = sliding_window(fqrec, qualtype, single_length_threshold, single_qual_threshold, no_fiveprime, trunc_n, drop_n, debug);
         total++;
 
         if (debug) printf("P1cut: %d,%d\n", p1cut->five_prime_cut, p1cut->three_prime_cut);