diff --git a/README.md b/README.md
index 35ab6a6..60cefd6 100644
--- a/README.md
+++ b/README.md
@@ -55,6 +55,7 @@ taxonomy ID. Additional options are specified below.
 Optional:
 *   `-o2, --output2 OUTPUT.FASTA.............`second output FASTA/Q file with extracted seqs (for paired reads)
 *   `--fastq-output..........................`Instead of producing FASTA files, print FASTQ files (requires FASTQ input)
+*   `--gzip-output...........................`Gzip output
 *   `--exclude...............................`Instead of finding reads matching specified taxids, finds reads NOT matching specified taxids.
 *   `-r, --report MYFILE.KREPORT.............`Kraken report file (required if specifying --include-children or --include-parents)
 *   `--include-children......................`include reads classified at more specific levels than specified taxonomy ID levels. 
diff --git a/combine_kreports.py b/combine_kreports.py
index 41d74ae..97bd6eb 100755
--- a/combine_kreports.py
+++ b/combine_kreports.py
@@ -54,6 +54,7 @@
 #   - main
 #   - process_kraken_report
 ####################################################################
+import gzip
 import os, sys, argparse
 import operator
 from time import gmtime 
@@ -197,8 +198,11 @@ def main():
         sys.stdout.write("\r\t%i/%i samples processed" % (count_samples, num_samples))
         sys.stdout.flush()
         id2files[count_samples] = r_file
-        #Open File 
-        curr_file = open(r_file,'r')
+        #Open File
+        if r_file.endswith(".gz"):
+            curr_file = gzip.open(r_file,'rt')
+        else:
+            curr_file = open(r_file, 'r')
         for line in curr_file: 
             report_vals = process_kraken_report(line)
             if len(report_vals) < 5:
diff --git a/extract_kraken_reads.py b/extract_kraken_reads.py
index d499fd7..8274d18 100755
--- a/extract_kraken_reads.py
+++ b/extract_kraken_reads.py
@@ -172,6 +172,8 @@ def main():
     parser.add_argument('--fastq-output', dest='fastq_out', required=False,
         action='store_true',default=False,
         help='Print output FASTQ reads [requires input FASTQ, default: output is FASTA]')
+    parser.add_argument('--gzip-output', dest='gzip_output', required=False,
+        action='store_true', default=False)
     parser.set_defaults(append=False)
 
     args=parser.parse_args()
@@ -343,13 +345,24 @@ def main():
     sys.stdout.flush()
     #Open output file
     if (args.append):
-        o_file = open(args.output_file, 'a')
-        if args.output_file2 != '':
-            o_file2 = open(args.output_file2, 'a')
+        if not args.gzip_output:
+            o_file = open(args.output_file, 'a')
+            if args.output_file2 != '':
+                o_file2 = open(args.output_file2, 'a')
+        else:
+            o_file = gzip.open(args.output_file, 'wta')
+            if args.output_file2 != '':
+                o_file2 = gzip.open(args.output_file2, 'wta')
     else:
-        o_file = open(args.output_file, 'w')
-        if args.output_file2 != '':
-            o_file2 = open(args.output_file2, 'w')
+        if not args.gzip_output:
+            o_file = open(args.output_file, 'w')
+            if args.output_file2 != '':
+                o_file2 = open(args.output_file2, 'w')
+        else:
+            o_file = gzip.open(args.output_file, 'wt')
+            if args.output_file2 != '':
+                o_file2 = gzip.open(args.output_file2, 'wt')
+ 
     #Process SEQUENCE 1 file 
     count_seqs = 0
     count_output = 0