\documentclass[tikz]{standalone}

\usepackage{luacode}
\usepackage{tikz}

\begin{document}

\begin{tikzpicture}
  \newcommand{\seqone}{TGCATA}
  \newcommand{\seqtwo}{ATCTGAT}
  \begin{luacode}
    local needle = require("needle")
    seq1 = \luastring{\seqone}
    seq2 = \luastring{\seqtwo}
    local tikz_code = needle.draw(seq1, seq2)
    tex.print(tikz_code)
  \end{luacode}
\end{tikzpicture}

\end{document}