diff --git a/Makefile.am b/Makefile.am
index a0120a3..c79401c 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -51,7 +51,6 @@ EXTRA_DIST = \
              docs/content/hmr-rep.md \
              docs/content/hypermr.md \
              docs/content/index.md \
-             docs/content/lc.md \
              docs/content/levels.md \
              docs/content/liftfilter.md \
              docs/content/merge-bsrate.md \
@@ -220,7 +219,6 @@ dnmtools_SOURCES += src/utils/guessprotocol.cpp
 dnmtools_SOURCES += src/utils/uniq.cpp
 dnmtools_SOURCES += src/utils/merge-bsrate.cpp
 dnmtools_SOURCES += src/utils/format-reads.cpp
-dnmtools_SOURCES += src/utils/lc-approx.cpp
 dnmtools_SOURCES += src/utils/selectsites.cpp
 dnmtools_SOURCES += src/utils/symmetric-cpgs.cpp
 dnmtools_SOURCES += src/utils/merge-methcounts.cpp
diff --git a/docs/content/lc.md b/docs/content/lc.md
deleted file mode 100644
index 703a009..0000000
--- a/docs/content/lc.md
+++ /dev/null
@@ -1,39 +0,0 @@
-# lc - Count number of lines in a big file
-
-## Synopsis
-```shell
-$ dnmtools lc <input-human-readable-file>
-```
-
-## Description
-
-When working with next-generation sequencing data, researchers often
-handle very large files, such as FASTQ files containing raw reads and
-\*.sam files containing mapped reads. `lc_approx` is an auxiliary tool
-designed to approximate the number of lines in a very large file by
-counting the number of lines in a small, randomly chosen chunk from
-the big file and scaling the estimate by file size. For example, in
-order to estimate the number of reads in a FASTQ file `input.fq`, run
-```shell
-$ dnmtools lc input.fq
-```
-It will return the approximate number of lines in this file and by
-dividing the above number by 4, you get the approximate number of
-reads in that file. The lc approx can be hundreds of times faster than
-the unix tool` wc -l`.
-
-## Options
-
-```txt
- -v, -verbose
-```
-print more run info to STDERR while the program is running.
-```txt
- -n, -samples
-```
-number of samples
-```txt
- -z, -size
-```
-sample size (bytes)
-
diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
index c38525a..0194111 100644
--- a/docs/mkdocs.yml
+++ b/docs/mkdocs.yml
@@ -42,7 +42,6 @@ nav:
    - General-purpose tools:
      - 'cleanhp': 'cleanhp.md'
      - 'guessprotocol': 'guessprotocol.md'
-     - 'lc': 'lc.md'
      - 'merge-bsrate': 'merge-bsrate.md'
      - 'merge': 'merge.md'
      - 'selectsites': 'selectsites.md'
diff --git a/src/dnmtools.cpp b/src/dnmtools.cpp
index 49b8df2..5ba9074 100644
--- a/src/dnmtools.cpp
+++ b/src/dnmtools.cpp
@@ -114,8 +114,6 @@ main_format(int argc, const char **argv);
 int
 main_guessprotocol(int argc, const char **argv);
 int
-main_lc_approx(int argc, const char **argv);
-int
 main_lift_filter(int argc, const char **argv);
 int
 main_merge_bsrate(int argc, const char **argv);
@@ -202,7 +200,6 @@ main(int argc, const char **argv) {
 {"utilities",
  {{{"cleanhp",       "fix and stat invdup/hairping reads", main_clean_hairpins},
    {"guessprotocol", "guess whether protocol is ordinary, pbat or random", main_guessprotocol},
-   {"lc",            "approximate line counts in a file", main_lc_approx},
    {"merge-bsrate",  "merge bisulfite conversion rates files from bsrate", main_merge_bsrate},
    {"merge",         "merge multiple counts files into a counts file or a table", main_merge_methcounts},
    {"covered",       "filter a counts file for only covered sites", main_covered},