Installing SAMtools on CentOS 7

SAMtools is a suite of programs for interacting with high-throughput sequencing data. SAMTools can be downloaded from http://www.htslib.org/download/

$ cd samtools-1.x # and similarly for bcftools and htslib
$ ./configure --prefix=/where/to/install
$ make
$ make install

In your .bashrc

export PATH=/where/to/install/bin:$PATH # for sh or bash users

Compile StringTie on CentOS 7.6

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.

System Information:

  • CentOS 7.6
  • GNU-4.8.5

The installation instruction can be found in the site

$ git clone https://github.com/gpertea/stringtie
$ cd stringtie
$ make release

Conduct Tests

$ ./run_tests.sh
..Downloading test data..
..unpacking test data..
Test 1: Short reads
OK.
Test 2: Short reads and super-reads
OK.
Test 3: Long reads
OK.
Test 4: Long reads with annotation guides
OK.