You can combine many of the above steps with simple one-liner! This is actually the preferred route, because you can install multiple tools at once, and ensure that conda installs compatible dependencies.conda create -n spadesEnv spades=3.11.1 bwa samtools fastqc ...
You can use Homebrew (brew) to install, uninstall, and upgrade any of thousands of “formulae” (i.e. package definitions) from its core public repository, plus any tap repositories you care to use. You can also use the Homebrew cask facility (brew-cask) as a way to install, uninstall...
install fakeroot libomp pulseaudio zimg fastqc libosmium pushpin znc ==> Deleted Formulae artifactory-cli-go boot2docker-completion ghc@8.0 gpg-agent wry boot2docker dirmngr gnupg@2.0 node@4 ==> Installing dependencies for wget: gettext, libunistring, libidn2, openssl ==> Installing wget ...
, always include a pre-processing step in which the raw reads are quality checked, trimmed, and cleaned, allowing reads to be used in the next steps. Widely accepted external tools for this step are, for example, FastQC, Cutadapt, and Trimommatic. In the next step, these clean sRNA ...