Repeatmasker
/uufs/chpc.utah.edu/common/home/u6007910/bin/RepeatMasker
Recon
/uufs/chpc.utah.edu/common/home/u6007910/bin/RepeatModeler-open-1.0.11/RECON-1.08/bin
RepeatScout
/uufs/chpc.utah.edu/common/home/u6007910/bin/RepeatModeler-open-1.0.11/RepeatScout-1
TRF
/uufs/chpc.utah.edu/common/home/u6007910/bin/RepeatModeler-open-1.0.11
nseg
/uufs/chpc.utah.edu/common/home/u6007910/bin/RepeatModeler-open-1.0.11/nseg
/uufs/chpc.utah.edu/common/home/u6007910/bin/RepeatMasker
BUSCO:
https://academic.oup.com/bioinformatics/article/31/19/3210/211866
QUAST:
https://academic.oup.com/bioinformatics/article/29/8/1072/228832
Installing BUSCO:
Requires working installation of Python 3, HMMER 3.1, Blast+,
Augustus (genome assessment only) and EMBOSS transeq (transcriptome assessment only).
Version available on CHPC:
Python version 3.5.2 (use module load python/3.5.2 to load and then say python to check version)
https://www.chpc.utah.edu/documentation/software/python.php
For HMMER 3.1:
This is installed in the bin directory (/uufs/chpc.utah.edu/common/home/u6007910/bin)
You don’t have to install HMMER programs to run them. The newly compiled binaries are now in the src directory. You can run them from there. To install the programs and man pages somewhere on your system, do:
> make install
By default, programs are installed in /usr/local/bin and man pages in /usr/local/share/man/man1/. You can change the /usr/local prefix to any directory you want using the ./configure --prefix option,
as in ./configure --prefix /the/directory/you/want.
Optionally, you can install the Easel library package as well, including its various “miniapplications”, in addition to its library and header files. We don’t do this by default, in case you already have a copy of Easel separately installed:
> cd easel; make install
That’s it. You can keep reading if you want to know more about customizing a HMMER installation, or you can skip ahead to the next chapter, the tutorial.