diff --git a/README.md b/README.md index a121406..b10342e 100644 --- a/README.md +++ b/README.md @@ -2,8 +2,7 @@ Identifies duplicate reads. This tool locates and tags duplicate reads in a coordinate ordered SAM or BAM file. -Use the same algorithm as picard MarkDuplicates and output identical results. -Use spdlog as log tool and the default level is 'info'. +Use the same algorithm as picard MarkDuplicates and output identical results, and use spdlog as log tool and the default level is 'info'. ### Features @@ -30,20 +29,13 @@ Use spdlog as log tool and the default level is 'info'. ## Requirements -### Build tools +Install following tools and required libraries. -* autoconf (for htslib) -* cmake -* c++17 (gcc >= 8.1 or clang >= 7 should work.) - -### Libraries needed - -* zlib -* libbz2 -* liblzma -* libcurl -* OpenSSL -* libdeflate (optional) +```bash +# install autoconf (for htslib), cmake, c++17 (gcc >= 8.1 or clang >= 7 should work), zlib, libbz2, liblzma, libcurl, libdeflate (optional) +sudo apt update +sudo apt install autoconf cmake g++-8 zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libdeflate-dev gcc-8 g++-8 +``` ## Install @@ -67,13 +59,13 @@ The generated binary fastdup will be in the build/bin folder. ## Usage -1. get help +Get help ```bash ./fastdup --help ``` -2. mark duplicates on an input BAM file using 8 threads +Mark duplicates on an input BAM file using 8 threads ```bash ./fastdup --input in_test.bam --output out_md.bam --metrics stats.txt --num-threads 8