diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..07c8369
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,11 @@
+*.a
+*.o
+bsmap
+samtools/bcftools/bcftools
+samtools/misc/maq2sam-long
+samtools/misc/maq2sam-short
+samtools/misc/md5fa
+samtools/misc/md5sum-lite
+samtools/misc/seqtk
+samtools/misc/wgsim
+samtools/samtools