diff --git a/src/cmdline.cpp b/src/cmdline.cpp
index 8328ac36..10275c59 100644
--- a/src/cmdline.cpp
+++ b/src/cmdline.cpp
@@ -28,6 +28,7 @@ CommandLineOptions parse_command_line_arguments(int argc, char **argv) {
     args::Flag no_progress(parser, "no-progress", "Disable progress report (enabled by default if output is a terminal)", {"no-progress"});
     args::Flag eqx(parser, "eqx", "Emit =/X instead of M CIGAR operations", {"eqx"});
     args::Flag x(parser, "x", "Only map reads, no base level alignment (produces PAF file)", {'x'});
+    args::Flag no_pg(parser, "no-PG", "Do not output PG header", {"no-PG"});
     args::Flag U(parser, "U", "Suppress output of unmapped reads", {'U'});
     args::Flag interleaved(parser, "interleaved", "Interleaved input", {"interleaved"});
     args::ValueFlag<std::string> rgid(parser, "ID", "Read group ID", {"rg-id"});
@@ -91,6 +92,7 @@ CommandLineOptions parse_command_line_arguments(int argc, char **argv) {
     if (v) { opt.verbose = true; }
     if (details) { opt.details = true; }
     if (no_progress) { opt.show_progress = false; }
+    if (no_pg) { opt.pg_header = false; }
     if (eqx) { opt.cigar_eqx = true; }
     if (x) { opt.is_sam_out = false; }
     if (U) { opt.output_unmapped = false; }
diff --git a/src/cmdline.hpp b/src/cmdline.hpp
index acb9e0b0..f3bf5265 100644
--- a/src/cmdline.hpp
+++ b/src/cmdline.hpp
@@ -22,6 +22,7 @@ struct CommandLineOptions {
     bool only_gen_index { false };
     bool use_index { false };
     bool is_sam_out { true };
+    bool pg_header { true };
     bool output_unmapped { true };
     int max_secondary { 0 };
 
diff --git a/src/main.cpp b/src/main.cpp
index 158e4954..e84587b1 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -33,7 +33,11 @@ static Logger& logger = Logger::get();
 /*
  * Return formatted SAM header as a string
  */
-std::string sam_header(const References& references, const std::string& read_group_id, const std::vector<std::string>& read_group_fields, const std::string& cmd_line) {
+std::string sam_header(
+    const References& references,
+    const std::string& read_group_id,
+    const std::vector<std::string>& read_group_fields
+) {
     std::stringstream out;
     out << "@HD\tVN:1.6\tSO:unsorted\n";
     for (size_t i = 0; i < references.size(); ++i) {
@@ -46,6 +50,11 @@ std::string sam_header(const References& references, const std::string& read_gro
         }
         out << '\n';
     }
+    return out.str();
+}
+
+std::string pg_header(const std::string& cmd_line) {
+    std::stringstream out;
     out << "@PG\tID:strobealign\tPN:strobealign\tVN:" << version_string() << "\tCL:" << cmd_line << std::endl;
     return out.str();
 }
@@ -280,7 +289,10 @@ int run_strobealign(int argc, char **argv) {
             cmd_line << argv[i] << " ";
         }
 
-        out << sam_header(references, opt.read_group_id, opt.read_group_fields, cmd_line.str());
+        out << sam_header(references, opt.read_group_id, opt.read_group_fields);
+        if (opt.pg_header) {
+            out << pg_header(cmd_line.str());
+        }
     }
 
     std::vector<AlignmentStatistics> log_stats_vec(opt.n_threads);
diff --git a/tests/run.sh b/tests/run.sh
index 097e64d1..dbdcb541 100755
--- a/tests/run.sh
+++ b/tests/run.sh
@@ -26,18 +26,18 @@ ${strobealign} -h > /dev/null
 samtools --version > /dev/null
 
 # Single-end SAM
-${strobealign} --eqx --chunk-size 3 --rg-id 1 --rg SM:sample --rg LB:library -v tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > phix.se.sam
+${strobealign} --no-PG --eqx --chunk-size 3 --rg-id 1 --rg SM:sample --rg LB:library -v tests/phix.fasta tests/phix.1.fastq > phix.se.sam
 diff tests/phix.se.sam phix.se.sam
 rm phix.se.sam
 
 # Single-end SAM, M CIGAR operators
-${strobealign} tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > phix.se.m.sam
+${strobealign} --no-PG tests/phix.fasta tests/phix.1.fastq > phix.se.m.sam
 if samtools view phix.se.m.sam | cut -f6 | grep -q '[X=]'; then false; fi
 
 rm phix.se.m.sam
 
 # Paired-end SAM
-${strobealign} --eqx --chunk-size 3 --rg-id 1 --rg SM:sample --rg LB:library tests/phix.fasta tests/phix.1.fastq tests/phix.2.fastq | grep -v '^@PG' > phix.pe.sam
+${strobealign} --no-PG --eqx --chunk-size 3 --rg-id 1 --rg SM:sample --rg LB:library tests/phix.fasta tests/phix.1.fastq tests/phix.2.fastq > phix.pe.sam
 diff tests/phix.pe.sam phix.pe.sam
 rm phix.pe.sam
 
@@ -57,9 +57,9 @@ diff tests/phix.pe.paf phix.pe.paf
 rm phix.pe.paf
 
 # Build a separate index
-${strobealign} -r 150 tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > without-sti.sam
+${strobealign} --no-PG -r 150 tests/phix.fasta tests/phix.1.fastq > without-sti.sam
 ${strobealign} -r 150 -i tests/phix.fasta
-${strobealign} -r 150 --use-index tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > with-sti.sam
+${strobealign} --no-PG -r 150 --use-index tests/phix.fasta tests/phix.1.fastq > with-sti.sam
 diff without-sti.sam with-sti.sam
 rm without-sti.sam with-sti.sam
 
@@ -73,8 +73,8 @@ ${strobealign} --details tests/phix.fasta tests/phix.1.fastq 2> /dev/null | samt
 # Secondary alignments
 
 # No secondary alignments on phix
-${strobealign} tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > no-secondary.sam
-${strobealign} -N 5 tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > with-secondary.sam
+${strobealign} --no-PG tests/phix.fasta tests/phix.1.fastq > no-secondary.sam
+${strobealign} --no-PG -N 5 tests/phix.fasta tests/phix.1.fastq > with-secondary.sam
 test $(samtools view -f 0x100 -c with-secondary.sam) -eq 0
 rm no-secondary.sam with-secondary.sam
 
@@ -82,8 +82,8 @@ rm no-secondary.sam with-secondary.sam
 cp tests/phix.fasta repeated-phix.fasta
 echo ">repeated_NC_001422" >> repeated-phix.fasta
 sed 1d tests/phix.fasta >> repeated-phix.fasta
-${strobealign} repeated-phix.fasta tests/phix.1.fastq | grep -v '^@PG' > no-secondary.sam
-${strobealign} -N 5 repeated-phix.fasta tests/phix.1.fastq | grep -v '^@PG' > with-secondary.sam
+${strobealign} --no-PG repeated-phix.fasta tests/phix.1.fastq > no-secondary.sam
+${strobealign} --no-PG -N 5 repeated-phix.fasta tests/phix.1.fastq > with-secondary.sam
 test $(samtools view -f 0x100 -c with-secondary.sam) -gt 0
 
 # Removing secondary alignments gives same result as not producing them in the first place